LECTURE 24 CHARMM course 21-MAR-2006
CHARMM ______
Chemistry at HARvard Molecular Mechanics ______
Twenty-Fourth Lecture: ______
Combined QM/MM Modeling and Simulation
Documentation qmmm.doc qchem.doc gamess.doc gamess-uk.doc sccdftb.doc mndo97.doc cadpac.doc diesel.doc charmmrate.doc cheq.doc flucq.doc
Examples ------None Available ------
No Homework Problem ______QM/MM Modeling Approach
● Couple quantum mechanics and molecular mechanics approaches (e.g. QM/MM)
● QM treatment of the active site – reacting center – excited state processes (e.g. spectroscopy) – problem structures (e.g. complex transition metal center)
● Classical MM treatment of environment – enzyme structure – explicit solvent molecules
– bulky organometallic ligan ds General QM/MM Methodology
● The QM/MM potential energy is implemented via solving the Schrödinger equation with an effective Hamiltonian
H eff r , Ra , RM = E Ra ,R M r , Ra , RM
● Where Heff and HQM/MM are defined as....
H eff = H QM H MM H QM / MM
qM Z A qM A A, M B A, M H QM / MM = −∑ ∑ ∑ 12 − 6 i , M ri M A, M R A, M A , M R A , M R A , M
● The total energy is then: 〈 ∣H QM H QM/ MM∣ 〉 Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227-249. Singh, U. C.; Kollman, P. A. J. Comp. Chem. 1986, 7, 718-730. Etot = EMM Field, M.J.; Bash, P.A.; Karplus, M. J. Comp. Chem. 1990, 11, 700-733. Lyne, P.D.; Hodoscek, M.; Karplus, M. J. Phys. Chem. A 1993, 103, 3462-3471. 〈∣ 〉 Eurenius, K.P.; Chatfield, D.C.; Brooks, B.R.; Hodoscek, M. Int. J. Quant. Chem. 1996, 60, 1189. Implementations of QM/MM Implementations of QM/MM Implementations of QM/MM
● Semi-empirical ● Pros: – AM1 – Fast – PM3 – Simpler than ab initio QM methods – MNDO – In many cases describes – PDP3 (PDDG/PM3) system(s) correctly – PDMN (PDDG/MNDO) ● Cons: – SCCDFTB – Reduced accuracy – Only restricted wavefunctions (caveat...) – Parameters – Ground state methods – Only valence electrons treated explicitly Implementations of QM/MM
● Ab initio ● Pros: – HF – Accuracy – DFT ● Much better description of wavefunction (e.g. ● Pure: BLYP correlation) ● Hybrid: B3LYP – Flexibility ● RI methods ● Cons: – MP2 – Performance ● Local methods ● Speed ● RI methods ● System size limitations – CCSD – More complex than semi- – Multireference methods empirical methods ● CASSCF ● Spin-flip ● EOM Additional Implementations of QM/MM
● Empirical Valence Bond ● SCCDFTB (EVB) – Empirical approximation to – Approximates QM DFT (B3LYP) interactions – QM/MM implementation – Mixes valence bond via CHARMM configurations – Approximately the same ● Must define bonding cost as AM1, PM3 patterns in “QM” ● But better accuracy system – Actively being developed – Requires parameterization ● Q. Cui ● M. Elstner Additional Implementations of QM/MM
● ONIOM: Morokuma et al. – QM/MM, QM/QM, QM/QM/MM and QM/QM/QM – Subtractive method
– Pro: Easy to use! – Widely available: Gaussian, Q-Chem 3.0 Additional Implementations of QM/MM
● CPMD: Car-Parrinello Molecular Dynamics – Employees DFT
● Mostly restricted to pure DFT functionals – QM wavefunction is propagated through the dynamics – Electronic motion can become coupled to the nuclear motion
● Should not happen in the Born-Oppenheimer approximation – Employees plane wave basis functions
● Needs a lot of them to describe the wave function accurately – Employees Effective Core Potentials (ECP) QM/MM Boundary Treatments QM/MM Boundary Treatments
● Single Link Atom (Singh and Kollman)
● Double Link Atom (Brooks and coworkers) – Gaussian Blur
● Generalized Hybrid Orbital (GHO) Approximation – Gao and coworkers
● Local Self-Consistent Field (LSCF) – Rivail and coworkers
● Frozen Orbital Approximation – Friesner and coworkers
● Pseudobond Methods – Yang and coworkers
Amara and Field; Theor Chem Acc (2003)109:43–52 QM/MM Boundary Treatments QM/MM Boundary Treatments
EXGR: QM/MM Electrostatics for link host groups removed Use CHARMM's lone pair facility to keep H (Link) atoms in proper orientation QM/MM Boundary Treatments QM/MM Boundary Treatments
DGMM: Delocalized Gaussian MM charges (e.g. Blurred Gaussian functions) QM/MM Boundary Treatments
Generalized Hybrid Orbital (GHO) Local Self-Consistent Field (LSCF)
Frozen Orbital Approximation Pseudobond Method CHARMM Element doc/qmmm.doc 1.1 # File: qmmm, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax
Combined Quantum and Molecular Mechanical Hamiltonian
A combined quantum (QM) and molecular (MM) mechanical potential allows for the study of condensed phase chemical reactions, reactive intermediates, and excited state isomerizations. This is necessary since standard MM force fields are parameterized with experimental data on the potential energy surface which may be far removed from the region of interest, or have the wrong analytical form. A full decription of the theory and application is given in J. Computational Chemistry (1990) 6, 700.
The effective Hamiltonian, Heff, describes the energy and forces on each atom. It is treated as a sum of four terms, Hqm, Hmm, Hqm/mm, and Hbrdy.
Hqm Describes the quantum mechanical particles. The semi- empirical methods available are AM1, PM3 and MNDO. All treat hydrogen, first row elements plus silicon, phosphorus, sulfur, and the halogens. MNDO has additional parameters for aluminium, phosphorus, chromium, germanium, tin, mercury, and lead. Full details concerning these theoretical methods can be found in Dewar's original papers, JACS (1985) 107, 3902, JACS (1977) 99, 4899, Theoret. Chim. Acta. (1977) 46, 89.
Hmm The molecular mechanical Hamiltonian is independent of the coordinates of the electrons and nuclei of the QM atoms. CHARMM22 is used to treat atoms in this region.
Hqm/mm The combined Hamiltonian describes how QM and MM atoms interact. This is composed of two electrostatic and one van der Waals terms. Each MM atom interacts with both the electrons and nuclei of the QM atoms (therefore two terms). The van der Waals term is necessary since some MM atoms possess no charge and would consequently be invisible to the QM atoms, and in other cases often provide the only difference in the interaction (Cl vs. Br).
Hbrdy The usual periodic or stochastic boundary conditions are implemented.
The quantum mechanical package MOPAC 4.0 was interfaced with CHARMM22. This was provided by James P. P. Stewart from the Air Force Academy. There are several limitations with the current program implemntation. The current plan is to update the quantum mechanical procedures to MOPAC 6.0, to include vibrational analysis using analytical functions, with the possibility of using free energy perturbation. * Menu:
1) QUANTUM module * Syntax:: Syntax of QM/MM Commands * Description:: Brief Description of Quantum Commands * GLINK:: GHO Method and GLNK Command * DECO:: DECO Command * DAMP:: DAMP Command * PERT:: PERT Command * pBOUNd:: Simple Periodic Boundary Condition * GROUp:: GROUp keyword * CHDYn:: CHDYn keyword * NEWD:: NEWDS Command * EXTE:: EXTErnal File Command * LEPS:: LEPS Command * SVB:: SVB Command * 2DSVB:: 2D Usage of SVB
2) SQUANTM module * SQUANTUM:: SQUANTUM Module * SQM_Syntax:: Syntax of the SQUANTM commands * SQM_Install:: Installation of SQUANTM in CHARMM environment
# File: qmmm, Node: Syntax, Up: Top, Previous: Top, Next: Description
Syntax for QUANTUM commands
QUANtum [atom-selection] [GLNK atom-selection] [LEPS int1 int2 int3] [DECO] [PERT REF0 lambda0 PER1 lambda1 PER2 lambda2 TEMP finalT] [NGUEss int] [NEWD int] ewald-spec
[IFIL int] [ITRMax int] [CAMP] [KING] [PULAy] [SHIFt real] [SCFCriteria real] [UHF] [C.I.] [EXCIted] [NMOS int] [MICR int] [TRIPLET|QUARTET|QUINTET|SEXTET]
[AM1|PM3|MNDO] [CHARge int] [NOCUtoff] [ALPM real] [RHO0 real] [SFT1 real] [EXCIted] [BIRADical] [C.I.]
[ITER] [EIG2] [ENERGY] [ PL ] [DEBUG [1ELEC] [DENSITY] [FOCK] [VECTor]]
[LEPS LEPA int LEPB int LEPC int D1AB real D1BC real D1AC real R1AB real R1BC real R1AC real B1AB real B1BC real B1AC real S1AB real S1BC real S1AC real D2AB real D2BC real D2AC real R2AB real R2BC real R2AC real B2AB real B2BC real B2AC real S2AB real S2BC real S2AC real] ewald-spec::= { [ KMAX integer ] } KSQMAX integer { KMXX integer KMXY integer KMXZ integer }
MULLiken
ADDLinkatom link-atom-name atom-spec atom-spec
RELLinkatom link-atom-name atom-spec atom-spec
link-atom-name ::= a four character descriptor starting with QQ.
atom-spec::= {residue-number atom-name} { segid resid atom-name } { BYNUm atom-number }
# File: qmmm, Node: Description, Up: Top, Previous: Syntax, Next: GLNK
Description of QUANtum Commands
Most keywords preceed an equal sign followed by an appropriate value. A description of each is given below.
1ELECtron The final one-electron matrix is printed out. This matrix is composed of atomic orbitals; the array element between orbitals i and j on different atoms is given by,
H(i,j) = 0.5 (beta(i) + beta(j)(overlap(i,j))
The matrix elements between orbitals i and j on the same atom are calculated from the electron-nuclear attraction energy, and also from the U(i) value if i=j.
The one-electron matrix is unaffected by (a) the charge and (b) the electron density. It is only a function of the geometry. Abbreviation: 1ELEC.
0SCF The data can be read in and output, but no actual calculation is performed when this keyword is used. This is useful as a check on the input data.
All obvious errors are trapped, and warning messages printed. A second use is to convert from one format to another. The input geometry is printed in various formats at the end of a 0SCF calculation. If NOINTER is absent, cartesian coordinates are printed. Unconditionally, MOPAC Z-matrix internal coordinates are printed, and if AIGOUT is present, Gaussian Z-matrix internal coordinates are printed. 0SCF should now be used in place of DDUM.
1SCF When users want to examine the results of a single SCF calculation of a geometry, 1SCF should be used. 1SCF can be used in conjunction with RESTART, in which case a single SCF calculation will be done, and the results printed.
When 1SCF is used on its own (that is, RESTART is not also used) then derivatives will only be calculated if GRAD is also specified. 1SCF is helpful in a learning situation. MOPAC normally performs many SCF calculations, and in order to minimize output when following the working of the SCF calculation, 1SCF is very useful.
AM1 The AM1 method is to be used. By default MNDO is run.
PM3 The PM3 method is to be used. By default MNDO is run.
NOCUtoff QM/MM cutoffs are disabled, such that the QM region interacts with all MM charges. By default the QM region only interacts with those charges that are within the standard CHARMM nonbond cutoffs.
ANALYTical By default, finite difference derivatives of energy with respect to geometry are used. If ANALYT is specified, then analytical derivatives are used instead. Since the analytical derivatives are over Gaussian functions -- a STO-6G basis set is used -- the overlaps are also over Gaussian functions. This will result in a very small (less than 0.1 Kcal/mole) change in heat of formation. Use analytical derivatives (a) when the mantissa used is less than about 51-53 bits, or (b) when comparison with finite difference is desired. Finite difference derivatives are still used when non-variationally optimized wavefunctions are present.
BIRADical NOTE: BIRADICAL is a redundant keyword, and represents a particular configuration interaction calculation. Experienced users of MECI (q.v.) can duplicate the effect of the keyword BIRADICAL by using the MECI keywords OPEN(2,2) and SINGLET. For molecules which are believed to have biradicaloid character the option exists to optimize the lowest singlet energy state which results from the mixing of three states. These states are, in order, (1) the (micro)state arising from a one electron excitation from the HOMO to the LUMO, which is combined with the microstate resulting from the time-reversal operator acting on the parent microstate, the result being a full singlet state; (2) the state resulting from de-excitation from the formal LUMO to the HOMO; and (3) the state resulting from the single electron in the formal HOMO being excited into the LUMO.
Microstate 1 Microstate 2 Microstate 3 Alpha Beta Alpha Beta Alpha Beta Alpha Beta
LUMO * * * * ------
+
HOMO * * * * ------
A configuration interaction calculation is involved here. A biradical calculation done without C.I. at the RHF level would be meaningless. Either rotational invariance would be lost, as in the D2d form of ethylene, or very artificial barriers to rotations would be found, such as in a methane molecule "orbiting" a D2d ethylene. In both cases the inclusion of limited configuration interaction corrects the error. BIRADICAL should not be used if either the HOMO or LUMO is degenerate; in this case, the full manifold of HOMO x LUMO should be included in the C.I., using MECI options. The user should be aware of this situation. When the biradical calculation is performed correctly, the result is normally a net stabilization. However, if the first singlet excited state is much higher in energy than the closed-shell ground state, BIRADICAL can lead to a destabilization. Abbreviation: BIRAD. See also MECI, C.I., OPEN, SINGLET.
CAMKINg
CHARge When the system being studied is an ion, the charge, n, on the ion must be supplied by CHARGE=n. For cations n can be 1 or 2 or 3, etc, for anions -1 or -2 or -3, etc.
EXAMPLES
ION KEYWORD ION KEYWORD
NH4(+) CHARGE=1 CH3COO(-) CHARGE=-1 C2H5(+) CHARGE=1 (COO)(=) CHARGE=-2 SO4(=) CHARGE=-2 PO4(3-) CHARGE=-3 HSO4(-) CHARGE=-1 H2PO4(-) CHARGE=-1
C.I. Normally configuration interaction is invoked if any of the keywords which imply a C.I. calculation are used, such as BIRADICAL, TRIPLET or QUARTET. Note that ROOT= does not imply a C.I. calculation: ROOT= is only used when a C.I. calculation is done. However, as these implied C.I.'s involve the minimum number of configurations practical, the user may want to define a larger than minimum C.I., in which case the keyword C.I.=n can be used. When C.I.=n is specified, the n M.O.'s which "bracket" the occupied- virtual energy levels will be used. Thus, C.I.=2 will include both the HOMO and the LUMO, while C.I.=1 (implied for odd-electron systems) will only include the HOMO (This will do nothing for a closed-shell system, and leads to Dewar's half-electron correction for odd-electron systems). Users should be aware of the rapid increase in the size of the C.I. with increasing numbers of M.O.'s being used. Numbers of microstates implied by the use of the keyword C.I.=n on its own are as follows:
Keyword Even-electron systems Odd-electron systems No. of electrons, configs No. of electrons, configs Alpha Beta Alpha Beta
C.I.=1 1 1 1 1 0 1 C.I.=2 1 1 4 1 0 2 C.I.=3 2 2 9 2 1 9 C.I.=4 2 2 36 2 1 24 C.I.=5 3 3 100 3 2 100 C.I.=6 3 3 400 3 2 300 C.I.=7 4 4 1225 4 3 1225 C.I.=8 (Do not use unless other keywords also used, see below)
If a change of spin is defined, then larger numbers of M.O.'s can be used up to a maximum of 10. The C.I. matrix is of size 100 x 100. For calculations involving up to 100 configurations, the spin-states are exact eigenstates of the spin operators. For systems with more than 100 configurations, the 100 configurations of lowest energy are used. See also MICROS and the keywords defining spin-states.
Note that for any system, use of C.I.=5 or higher normally implies the diagonalization of a 100 by 100 matrix. As a geometry optimization using a C.I. requires the derivatives to be calculated using derivatives of the C.I. matrix, geometry optimization with large C.I.'s will require more time than smaller C.I.'s.
Associated keywords: MECI, ROOT=, MICROS, SINGLET, DOUBLET, etc.
C.I.=(n,m) In addition to specifying the number of M.O.'s in the active space, the number of electrons can also be defined. In C.I.=(n,m), n is the number of M.O.s in the active space, and m is the number of doubly filled levels to be used.
EXAMPLES Keywords Number of M.O.s No. Electrons
C.I.=2 2 2 (1) C.I.=(2,1) 2 2 (3) C.I.=(3,1) 3 2 (3) C.I.=(3,2) 3 4 (5) C.I.=(3,0) OPEN(2,3) 3 2 (N/A) C.I.=(3,1) OPEN(2,2) 3 4 (N/A) C.I.=(3,1) OPEN(1,2) 3 N/A (3)
Odd electron systems given in parentheses.
DEBUG Certain keywords have specific output control meanings, such as FOCK, VECTORS and DENSITY. If they are used, only the final arrays of the relevant type are printed. If DEBUG is supplied, then all arrays are printed. This is useful in debugging ITER. DEBUG can also increase the amount of output produced when certain output keywords are used, e.g. COMPFG.
DCART The cartesian derivatives which are calculated in DCART for variationally optimized systems are printed if the keyword DCART is present. The derivatives are in units of kcals/Angstrom, and the coordinates are displacements in x, y, and z.
DENSITY At the end of a job, when the results are being printed, the density matrix is also printed. For RHF the normal density matrix is printed. For UHF the sum of the alpha and beta density matrices is printed. If density is not requested, then the diagonal of the density matrix, i.e., the electron density on the atomic orbitals, will be printed.
DOUBLet When a configuration interaction calculation is done, all spin states are calculated simultaneously, either for component of spin = 0 or 1/2. When only doublet states are of interest, then DOUBLET can be specified, and all other spin states, while calculated, are ignored in the choice of root to be used.
Note that while almost every odd-electron system will have a doublet ground state, DOUBLET should still be specified if the desired state must be a doublet.
DOUBLET has no meaning in a UHF calculation.
EIGS EIG2 ENERGY
ESR The unpaired spin density arising from an odd-electron system can be calculated both RHF and UHF. In a UHF calculation the alpha and beta M.O.'s have different spatial forms, so unpaired spin density can naturally be present on in-plane hydrogen atoms such as in the phenoxy radical.
In the RHF formalism a MECI calculation is performed. If the keywords OPEN and C.I.= are both absent then only a single state is calculated. The unpaired spin density is then calculated from the state function. In order to have unpaired spin density on the hydrogens in, for example, the phenoxy radical, several states should be mixed.
EXCIted The state to be calculated is the first excited open-shell singlet state. If the ground state is a singlet, then the state calculated will be S(1); if the ground state is a triplet, then S(2). This state would normally be the state resulting from a one-electron excitation from the HOMO to the LUMO. Exceptions would be if the lowest singlet state were a biradical, in which case the EXCITED state could be a closed shell.
The EXCITED state will be calculated from a BIRADICAL calculation in which the second root of the C.I. matrix is selected. Note that the eigenvector of the C.I. matrix is not used in the current formalism. Abbreviation: EXCI.
NOTE: EXCITED is a redundant keyword, and represents a particular configuration interaction calculation. Experienced users of MECI can duplicate the effect of the keyword EXCITED by using the MECI keywords OPEN(2,2), SINGLET, and ROOT=2.
FOCK FORCE A force-calculation is to be run. The Hessian, that is the matrix (in millidynes per Angstrom) of second derivatives of the energy with respect to displacements of all pairs of atoms in x, y, and z directions, is calculated. On diagonalization this gives the force constants for the molecule. The force matrix, weighted for isotopic masses, is then used for calculating the vibrational frequencies. The system can be characterized as a ground state or a transition state by the presence of five (for a linear system) or six eigenvalues which are very small (less than about 30 reciprocal centimeters). A transition state is further characterized by one, and exactly one, negative force constant.
A FORCE calculation is a prerequisite for a THERMO calculation. Before a FORCE calculation is started, a check is made to ensure that a stationary point is being used. This check involves calculating the gradient norm (GNORM) and if it is significant, the GNORM will be reduced using BFGS.
All internal coordinates are optimized, and any symmetry constraints are ignored at this point. An implication of this is that if the specification of the geometry relies on any angles being exactly 180 or zero degrees, the calculation may fail.
The geometric definition supplied to FORCE should not rely on angles or dihedrals assuming exact values. (The test of exact linearity is sufficiently slack that most molecules that are linear, such as acetylene and but-2-yne, should not be stopped.) See also THERMO, LET, TRANS, ISOTOPE.
In a FORCE calculation, PRECISE will eliminate quartic contamination (part of the anharmonicity). This is normally not important, therefore PRECISE should not routinely be used.
In a FORCE calculation, the SCF criterion is automatically made more stringent; this is the main cause of the SCF failing in a FORCE calculation.
ITER The default maximum number of SCF iterations is 200. When this limit presents difficulty, ITRY=nn can be used to re-define it. For example, if ITRY=400 is used, the maximum number of iterations will be set to 400. ITRY should normally not be changed until all other means of obtaining a SCF have been exhausted, e.g. PULAY CAMP-KING etc.
INTERP LPULAY
LARGE Most of the time the output invoked by keywords is sufficient. LARGE will cause less-commonly wanted, but still useful, output to be printed.
1. To save space, DRC and IRC outputs will, by default, only print the line with the percent sign. Other output can be obtained by use of the keyword LARGE, according to the following rules:
Keyword Effect LARGE Print all internal and cartesian coordinates and cartesian velocities. LARGE=1 Print all internal coordinates. LARGE=-1 Print all internal and cartesian coordinates and cartesian velocities. LARGE=n Print every n'th set of internal coordinates. LARGE=-n Print every n'th set of internal and cartesian coordinates and cartesian velocities.
If LARGE=1 is used, the output will be the same as that of Version 5.0, when LARGE was not used. If LARGE is used, the output will be the same as that of Version 5.0, when LARGE was used. To save disk space, do not use LARGE.
MECI At the end of the calculation details of the Multi Electron Configuration Interaction calculation are printed if MECI is specified. The state vectors can be printed by specifying VECTORS. The MECI calculation is either invoked automatically, or explicitly invoked by the use of the C.I.=n keyword.
MICRos The microstates used by MECI are normally generated by use of a permutation operator. When individually defined microstates are desired, then MICROS=n can be used, where n defines the number of microstates to be read in.
Format for Microstates
After the geometry data plus any symmetry data are read in, data defining each microstate is read in, using format 20I1, one microstate per line. The microstate data is preceded by the word "MICROS" on a line by itself. There is at present no mechanism for using MICROS with a reaction path.
For a system with n M.O.'s in the C.I. (use OPEN=(n1,n) or C.I.=n to do this), the populations of the n alpha M.O.'s are defined, followed by the n beta M.O.'s. Allowed occupancies are zero and one. For n=6 the closed-shell ground state would be defined as 111000111000, meaning one electron in each of the first three alpha M.O.'s, and one electron in each of the first three beta M.O.'s.
Users are warned that they are responsible for completing any spin manifolds. Thus while the state 111100110000 is a triplet state with component of spin = 1, the state 111000110100, while having a component of spin = 0 is neither a singlet nor a triplet. In order to complete the spin manifold the microstate 110100111000 must also be included.
If a manifold of spin states is not complete, then the eigenstates of the spin operator will not be quantized. When and only when 100 or fewer microstates are supplied, can spin quantization be conserved.
There are two other limitations on possible microstates. First, the number of electrons in every microstate should be the same. If they differ, a warning message will be printed, and the calculation continued (but the results will almost certainly be nonsense). Second, the component of spin for every microstate must be the same, except for teaching purposes. Two microstates of different components of spin will have a zero matrix element connecting them. No warning will be given as this is a reasonable operation in a teaching situation. For example, if all states arising from two electrons in two levels are to be calculated say for teaching Russel-Saunders coupling, then the following microstates would be used:
Microstate No. of alpha, beta electrons Ms State
1100 2 0 1 Triplet 1010 1 1 0 Singlet 1001 1 1 0 Mixed 0110 1 1 0 Mixed 0101 1 1 0 Singlet 0011 0 2 -1 Triplet
Constraints on the space manifold are just as rigorous, but much easier to satisfy. If the energy levels are degenerate, then all components of a manifold of degenerate M.O.'s should be either included or excluded. If only some, but not all, components are used, the required degeneracy of the states will be missing.
As an example, for the tetrahedral methane cation, if the user supplies the microstates corresponding to a component of spin = 3/2, neglecting Jahn-Teller distortion, the minimum number of states that can be supplied is 90 = (6!/(1!*5!))* (6!/(4!*2!)).
While the total number of electrons should be the same for all microstates, this number does not need to be the same as the number of electrons supplied to the C.I.; thus in the example above, a cationic state could be 110000111000.
The format is defined as 20I1 so that spaces can be used for empty M.O.'s.
MNDO The default Hamiltonian within MOPAC is MNDO, with the alternatives of AM1 and MINDO/3. To use the MINDO/3 Hamiltonian the keyword MINDO/3 should be used. Acceptable alternatives to the keyword MINDO/3 are MINDO and MINDO3.
NGUEss The number of steps to regenerate initial guess during molecular dynamics. The default is 100 step. If NGUEss <= 0, then it will be used previous density all over the dynamics. Only applied in the molecular dynamics.
PRECISE The criteria for terminating all optimizations, electronic and geometric, are to be increased by a factor, normally, 100. This can be used where more precise results are wanted. If the results are going to be used in a FORCE calculation, where the geometry needs to be known quite precisely, then PRECISE is recommended; for small systems the extra cost in CPU time is minimal.
PRECISE is not recommended for experienced users, instead GNORM=n.nn and SCFCRT=n.nn are suggested. PRECISE should only very rarely be necessary in a FORCE calculation: all it does is remove quartic contamination, which only affects the trivial modes significantly, and is very expensive in CPU time.
PULAy The default converger in the SCF calculation is to be replaced by Pulay's procedure as soon as the density matrix is sufficiently stable. A considerable improvement in speed can be achieved by the use of PULAY. If a large number of SCF calculations are envisaged, a sample calculation using 1SCF and PULAY should be compared with using 1SCF on its own, and if a saving in time results, then PULAY should be used in the full calculation. PULAY should be used with care in that its use will prevent the combined package of convergers (SHIFT, PULAY and the CAMP-KING convergers) from automatically being used in the event that the system fails to go SCF in (ITRY-10) iterations.
The combined set of convergers very seldom fails.
QUARTet RHF interpretation: The desired spin-state is a quartet, i.e., the state with component of spin = 1/2 and spin = 3/2. When a configuration interaction calculation is done, all spin states of spin equal to, or greater than 1/2 are calculated simultaneously, for component of spin = 1/2. From these states the quartet states are selected when QUARTET is specified, and all other spin states, while calculated, are ignored in the choice of root to be used. If QUARTET is used on its own, then a single state, corresponding to an alpha electron in each of three M.O.'s is calculated.
UHF interpretation: The system will have three more alpha electrons than beta electrons.
QUINTet RHF interpretation: The desired spin-state is a quintet, that is, the state with component of spin = 0 and spin = 2. When a configuration interaction calculation is done, all spin states of spin equal to, or greater than 0 are calculated simultaneously, for component of spin = 0. From these states the quintet states are selected when QUINTET is specified, and the septet states, while calculated, will be ignored in the choice of root to be used. If QUINTET is used on its own, then a single state, corresponding to an alpha electron in each of four M.O.'s is calculated.
UHF interpretation: The system will have three more alpha electrons than beta electrons.
ROOT The n'th root of a C.I. calculation is to be used in the calculation. If a keyword specifying the spin-state is also present, e.g. SINGLET or TRIPLET, then the n'th root of that state will be selected. Thus ROOT=3 and SINGLET will select the third singlet root. If ROOT=3 is used on its own, then the third root will be used, which may be a triplet, the third singlet, or the second singlet (the second root might be a triplet). In normal use, this keyword would not be used. It is retained for educational and research purposes. Unusual care should be exercised when ROOT= is specified.
SCFCrt The default SCF criterion is to be replaced by that defined by SCFCRT=. The SCF criterion is the change in energy in kcal/mol on two successive iterations. Other minor criteria may make the requirements for an SCF slightly more stringent. The SCF criterion can be varied from about 0.001 to 1.D-25, although numbers in the range 0.0001 to 1.D-9 will suffice for most applications.
An overly tight criterion can lead to failure to achieve a SCF, and consequent failure of the run.
SEXTet RHF interpretation: The desired spin-state is a sextet: the state with component of spin = 1/2 and spin = 5/2. The sextet states are the highest spin states normally calculable using MOPAC in its unmodified form. If SEXTET is used on its own, then a single state, corresponding to one alpha electron in each of five M.O.'s, is calculated. If several sextets are to be calculated, say the second or third, then OPEN(n1,n2) should be used.
UHF interpretation: The system will have five more alpha electrons than beta electrons.
SHIFt In an attempt to obtain an SCF by damping oscillations which slow down the convergence or prevent an SCF being achieved, the virtual M.O. energy levels are shifted up or down in energy by a shift technique. The principle is that if the virtual M.O.'s are changed in energy relative to the occupied set, then the polarizability of the occupied M.O.'s will change pro rata. Normally, oscillations are due to autoregenerative charge fluctuations.
The SHIFT method has been re-written so that the value of SHIFT changes automatically to give a critically-damped system. This can result in a positive or negative shift of the virtual M.O. energy levels. If a non-zero SHIFT is specified, it will be used to start the SHIFT technique, rather than the default 15eV. If SHIFT=0 is specified, the SHIFT technique will not be used unless normal convergence techniques fail and the automatic "ALL CONVERGERS..." message is produced.
SINGLet When a configuration interaction calculation is done, all spin states are calculated simultaneously, either for component of spin = 0 or 1/2. When only singlet states are of interest, then SINGLET can be specified, and all other spin states, while calculated, are ignored in the choice of root to be used.
Note that while almost every even-electron system will have a singlet ground state, SINGLET should still be specified if the desired state must be a singlet.
SINGLET has no meaning in a UHF calculation, but see also TRIPLET.
TRIPLet The triplet state is defined. If the system has an odd number of electrons, an error message will be printed.
UHF interpretation. The number of alpha electrons exceeds that of the beta electrons by 2. If TRIPLET is not specified, then the numbers of alpha and beta electrons are set equal. This does not necessarily correspond to a singlet.
RHF interpretation.
An RHF MECI calculation is performed to calculate the triplet state. If no other C.I. keywords are used, then only one state is calculated by default. The occupancy of the M.O.'s in the SCF calculation is defined as (...2,1,1,0,..), that is, one electron is put in each of the two highest occupied M.O.'s.
See keywords C.I.=n and OPEN(n1,n2).
UHF The unrestricted Hartree-Fock Hamiltonian is to be used.
VECTors The eigenvectors are to be printed. In UHF calculations both alpha and beta eigenvectors are printed; in all cases the full set, occupied and virtual, are output. The eigenvectors are normalized to unity, that is the sum of the squares of the coefficients is exactly one. If DEBUG is specified, then ALL eigenvectors on every iteration of every SCF calculation will be printed. This is useful in a learning context, but would normally be very undesirable.
# File: qmmm, Node: GLNK, Up: Top, Previous: Description, Next: DECO
Description of the Generalized Hybrid Orbital (GHO) method and the GLNK Command
[GLNK atom-selection] atom-selection: contains a list of atoms that are boundary atoms.
Restrictions: The current implementation of the method requires that ALL boundary atoms are placed at the end of the QM residue, or at the end of the QM atom list. It is also strongly advised to treat the entire QM fragment as a single residue, without any GROUPping of atoms. This is because the delocalized nature of molecular orbitals does not allow for arbitrarily excluding a particular fragment or orbitals from interacting with other parts of the system.
Description: In addition to the link atom approach, a generalized hybrid orbital (GHO) approach for the treatment of the division across a covalent bond between the QM and MM region. The method recognizes a frontier atom, typically carbon which is the only atom that has its parameters optimized at this time, both as a QM atom and an MM atom. Thus, standard basis orbitals are assigned to this atom. These atomic orbitals on the frontier atoms are transformed into a set of equivalent hybrid orbitals (typically the frontier atom is of sp3 hybridization type). One of the four hybrid orbitals, which points directly to the direction of the neighboring QM atom, is included in QM-SCF orbital optimizations, and is an active orbital. The other three hybrid orbitals are not optimized. Thus, they are the auxillary orbitals. Since hybridization (contributions from s and p orbitals to the hybrid orbitals) is dependent on the local geometry, change of bond angles will lead to bond polarization in the active orbital. Also, since the active orbital is being optimized in the SCF procedure, charge transfer between the frontier atom and the QM fragment is allowed. Consequently, the GHO method provides a convenient way for smooth transition of charge distribution from the QM region into the MM region.
The charge density on the auxilary orbitals are determined by equally distributing the MM partial charge on the frontier atom. Thus, P(mu mu) = 1 - q(mm)/3. The neutral group convention adopted by the CHARMM force field makes it possible not to alter, to add, or to delete any MM charges. Furthermore, no extra degrees of freedom is introduced in the GHO approach.
The GHO method based on Unrestricted HF theory (GHO-UHF) is implemented at semiempirical level (AM1, PM3) in the quantum module. With this extension, GHO boundary treatment can be used for open shell QM fragments in combined QM/MM calculations.
For a GHO-UHF wavefunction, we have two sets of auxiliary hybrid orbitals for alpha spin and beta spin electrons respectively. The charge density assigned to each of these auxiliary hybrid orbitals is 0.5(1.0-q(mm)/3.0), while q(mm) denotes the MM partial charge of the GHO boundary atom. Similar to GHO-RHF, the hybridization basis transformation is carried out between the density matrix and Fock matrix, both for the alpha and the beta sets.
Analytical gradients and Mulliken population analysis are also implemented for GHO- UHF.
Limitations: The present implementation allows up to 5 QM-boundary atoms, which uses psuedo-atomic numbers 91-95. Thus, elements 91 through 95 can not be used in QM calculations.
Reference: Reference made to the following paper, which contains a more thorough description and discussion of test cases, is appreciated.
Jiali Gao, Patricia Amara, Cristobal Alhambra, and Martin J. Field, J. Phys. Chem. 102, 4714-4721 (1998). "A Generalized Hybrid Orbital (GHO) Approach for the Treatment of Link-Atoms using Combined QM/MM Potentials."
# File: qmmm, Node: DECO, Up: Top, Previous: GLNK, Next: DAMP
Description of the DECO Command
[DECO]
The lone command DECO initiates an qm/mm interaction energy decomposition calculation on the fly during a molecular dynamics simulation using the QUANtum command. It is currently implemented only for semiempirical Hamiltonians. The analysis is based on the method reported in J. Gao and X. Xia, Science, 258, 631 (1992). It decomposes the total QM/MM electrostatic interaction energy into a vertical interaction energy Evert, and a polarization term Epol. The latter is further separated into electrostatic stabilization Estab, and charge distortion Edist. These terms are defined as follows (Y is the wave function of the qm system in the presence of mm charges, and Yo is the wave function of the qm system in the absence of mm charges, i.e., in the gas phase): Eqm/mm =
Epol = Estab + Edist Estab =
# File: qmmm, Node: DAMP, Up: Top, Previous: DECO, Next: PERT
[ DAMP real ]
A simple density damping option is added to the SCF driver for the quantum module. The motivation of adding this option is to provide a possibility to overcome SCF convergence difficulties. Currently, this damping accelerator is only used to limit oscillation behavior in GHO-UHF type calculations.
For an SCF iteration with density damping turned on, the actual density matrix used for next iteration is computed by a linear combination of the current density with the previous one:
P = a x P + (1-a) x P i i-1 i
The damping factor "a" is a user defined floating point number between 0 and 1. One can specify this damping factor as "DAMP a" in the QUANtum command line. The default of this damping factor is 0.0, i.e., no damping at all. Any damping factor being less than 0 or greater than 1 will incur a level -5 warning.
In the current implementation, several "damped" steps (with a user defined damping factor "a" ) are carried out until the alpha and beta density matrices are partially converged (density changes are smaller than 100 times the density convergence criterion), then "undamped" steps (a=0.0) follow until the final convergence is reached.
# File: qmmm, Node: PERT, Up: Top, Previous: DAMP, Next: pBOUND
Description of the PERT Command
[PERT REF0 lambda0 PER1 lambda1 PER2 lambda2 TEMP finalT]
REF0 lambda0 the reference Lambda value in a FEP calculation PER1 lambda1 the forward perturbation Lambda value in a FEP calculation PER2 lambda2 the reverse perturbation Lambda value in a FEP calculation TEMP finalT the target or final temperature of the MD simulation NOTE: this is required. Otherwise an error will occur.
The PERT command performs electrostatic free energy decoupling calculation for QM/MM interactions on the fly of a molecular dynamics simulation. The algorithm is based on a method described in J. Gao, J. Phys. Chem. 96, 537 (1992). Through a series of simulations, the electrostatic component of the free energy of solvation can be determined. See, other free energy simulation documents.
Delta G(L0->L1) = -RT < exp(-[E{H(L1)}-E{H(L0)}]/RT > _E{H(L0)} where
E{H(Li)} =
JG 12/00
# File: qmmm, Node: pBOUNd, Up: Top, Previous: PERT Description, Next: GROUp
Simple Periodic Boundary Conditions for QM/MM calculations
This code is an extension of the algorithm already implemented in CHARMM for MM calculations. The reason for making this extention is to avoid duplication of coordinates to save memory in QM/MM calculations. It takes advantage of the minimum image convention for a periodic cubic (or rectangular or any other shapes) box such that crystallographic images are not required to be generated in the psf (see images.doc).
[Syntax]
BOUNd {CUBOUNdary } {BOXL
CUBOUN = CUbicBOUNd BOXL = length of the box edge CUTNB = cutoff for generating "virtual" images
Note: QM/MM PBOUND is INCOMPATIBLE with atom based non-bonded list.
RESTRICTIONS:
1. Information about the periodic boundary must be given to the program through the command READ IMAGE (see image.doc)
2. The system must be centered using commands: a) IMAGE (see image.doc) when solute and solvent are small molecules (3-5 atoms) b) CENT keyword in DYNA command line (see dynamc.doc) when solute is a protein or large organic molecule.
3. The mm and qm/mm nonbonded lists (electrostatic and Van der Waals interactions) must be generated by groups, i.e:
update group fswitch vdw vswitched vgroup ... 4. Compile with PBOUND in pref.dat
Example: ...
! Set-up image information for cubic periodic boundaries ! cubig.img file in the /test/data/ directory set 6 58.93044 set 7 58.93044 set 8 58.93044 open unit 1 read form name cubic.img read image card unit 1 close unit 1
IMAGe byseg xcen 0.0 ycen 0.0 zcen 0.0 select segid prot end IMAGe byres xcen 0.0 ycen 0.0 zcen 0.0 select sol end
BOUNd CUBOUND BOXL 58.93044 CUTNB 12.0
UPDAte group fswitch noextend cdie vdw vswitched eps 1.0 - cutnb 12.0 ctofnb 11.5 ctonnb 10.5 vgroup WMIN 1.2 - inbf 25 imgfrq 1000 cutim 12.0
QUANtum group sele qms end glnk sele bynu 68:69 end am1 charge 1 - scfc 0.000001
DYNAmics vverlet rest nstep 15000 timestp 0.001 - ilbfrq 0 iseed 324239 firstt 239.0 finalt 298.15 - teminc 5.0 ihtfrq 5.0 iasor 0 iasvel 1 iscvel 0 - ichecw 1 ieqfrq 200 nprint 100 nsavc 00 - nose tref 298.15 qref 50.0 isvfrq 100 - tstruc 298.15 - twindh 5 twindl -5 iprfrq 2000 wmin 0.9 - iunrea 9 iunwri 10 iuncrd 11 iunvel -1 kunit -12 - CENT ncres 162
....
# File: qmmm, Node: GROUp, Up: Top, Previous: pBOUNd , Next: CHDYn
Description of the GROUp keyword
[ GROUp]
The QM/MM module that was initially implemented into CHARMM allows for separate QM group and MM group interactions, where a "QM" molecule can be divided into several groups. The GROUp option allows the QM molecule to be partitioned into separate groups for generating non-bonded list, but keeps the interactions between the ENTIRE QM molecule and any MM group that is whithin the cutoff of any one qm group, avoiding the possibility that some MM group only interact with part of the QM molecule. This is necessary because the QM molecule is not divisible as the wave function is delocalized over the entire molecule. (June, 2001) See also description of the GLNK keyword.
# File: qmmm, Node: CHDYn, Up: Top, Previous: GROUp , Next: NEWD
Description of the CHDYn keyword
[CHDYn]
CHDYn allows the computation of average Mulliken population charges on quantum atoms during a molecular dynamics simulation. It prints the averaged atomic charges at every IPRFRQ steps. When CHDYn is used along with DECO it will result in the calculation of average atomic charges for the same trajectory in the presence of the MM bath (condensed phase) and absence of the MM charges (gas phase).
RESTRICTIONS: CHDYn is only implemented for molecular dynamics calculations with the Leapfrog Verlet and Velocity Verlet integrators.
TESTCASE : qmfep.inp
# File: qmmm, Node: NEWD, Up: Top, Previous: CHDYn, Next: EXTE
Description of the NEWDS Command
[ NEWD int ] ewald-spec
ewald-spec::= { [ KMAX integer ] } KSQMAX integer { KMXX integer KMXY integer KMXZ integer }
A simple Ewald sum method is implemented into the QM/MM potential. A full description of theory is described in J. Chem. Theory. Comput. (2005) 1, 2. This is based on regular Ewald sum method and share similar keywords (see ewald.doc).
The defaults for the QM/MM-Ewald calculations are set internally and are currently set to NEWD 1, KMAX=5, KSQMax=27, where the KMAX keyword is the number of kvectors (or images of the primary unit cell) that will be summed in any direction. It is the radius of the Ewald summation. For orthorombic cells, the value of kmax may be independently specified in the x, y, and z directions with the keywords KMXX, KMXY, and KMXZ. But, different from regular Ewald in CHARMM, it has no limitation on the shape of box, and can be used with PMEwald in MM part.
The KSQMax key word should be chosen between KMAX squared and 3 times KMAX squared, and KAPPA value share the exact same number you use in Nonbond options.
# File: qmmm, Node: EXTE, Up: Top, Previous: NEWD, Next: LEPS
[EXTErnal PUNIt int]
EXTE Allows reading the semi-empirical parameters from an external file. The format is as follows (free format):
PARNAME1 ATOMTYPE1 PARVALUE1 PARNAME2 ATOMTYPE2 PARVALUE2 ... END
Empty lines are ignored Acceptable parameters names are: ALFA(ALP),BETAS,BETAP,BETAD,ZS,ZP,ZD,USS,UPP,UDD,GSS,GPP,GSP,GP2,HSP, VS,VP,K1(FN11),L1(FN21),M1(FN31),K2(FN12),L2(FN22),M2(FN32),K3(FN13), L3(FN23),M3(FN33),K4(FN14),L4(FN24),M4(FN34)
The following derived parameters are computed automatically: EISOL,DD,QQ,AM,AD,AQ
Example: USS H -11.3336021333 BETAS H -6.1735981344 END
# File: qmmm, Node: LEPS, Up: Top, Previous: EXTE, Next: SVB
Description of the LEPS Command
[LEPS LEPA int LEPB int LEPC int - D1AB real D1BC real D1AC real - R1AB real R1BC real R1AC reat - B1AB real B1BC real B1AC real - S1AB real S1BC real S1AC real - D2AB real D2BC real D2AC real - R2AB real R2BC real R2AC real - B2AB real B2BC real B2AC real - S2AB real S2BC real S2AC real]
Description: The motivation behind the semiempirical valence bond term (SEVB) is to improve the quality of the potential energy surface (PES) when using semiempirical hamiltonians (AM1 or PM3) to model the reactive event in enzyme active sites. NDDO based hamiltonias represent a cheap alternative to describe reactions in enzyme active sites. They allow for a quantum mechanical description of the active site together with an extensive sampling of the protein configurational space when combined qmm/mm techniques are used. However the savings in computer time come with sacrifices in the quality of the PES due to the NDDO approximation. The SEVB term is introduced in the hamiltonian of the system to palliate this problem. It contains two extended London-Eiring-Polany-Sato (LEPS) equations for the three body subsystem {A,B,C}. This reduced subsystem mimics the transfer of the particle B between centers A and C in the active site. In most of the applications B is a light atom like hydrogen and A and C correspond to the donor and acceptor sites,
A-B + C ---> A + B-C
Each of the two extended LEPS functions have different parameters and depend on the distances r(A-B), r(B-C), and r(A-C). One LEPS potential (V(ref))is fitted to reproduce high ab initio or experimental data for a model reaction whilst the second one (V(NDDO)) is fitted to the NDDO hamiltonian in use. Finally the SEVB correction is introduced in the hamiltonian of the system as the difference V(ref)-V(NDDO).
Syntaxis: The keyword LEPS in the command line QUANtum turns on the routine that evaluates the SEVB correction. The three atoms needed to evaluate the distances r(A-B), r(B-C), and r(A-C) are indicated by,
LEPA - donor center. LEPB - transferred atom. LEPC - acceptor center.
int - corresponds to the psf number of the respective atom.
The value of the parameters to build the functions V(NDDO) and V(ref) are,
. for the NDDO LEPS functions,
D1AB - dissociation energy for the diatomic A-B D1BC - dissociation energy for the diatomic B-C D1AC - dissociation energy for the diatomic A-C R1AB - equilibrium distance for the diatomic A-B R1BC - equilibrium distance for the diatomic B-C R1AC - equilibrium distance for the diatomic A-C B1AB - beta exponent for the diatomic A-B B1BC - beta exponent for the diatomic B-C B1AC - beta exponent for the diatomic A-C S1AB - Sato parameter for the diatomic A-B S1BC - Sato parameter for the diatomic B-C S1AC - Sato parameter for the diatomic A-C
. for the reference LEPS functions,
D2AB - dissociation energy for the diatomic A-B D2BC - dissociation energy for the diatomic B-C D2AC - dissociation energy for the diatomic A-C R2AB - equilibrium distance for the diatomic A-B R2BC - equilibrium distance for the diatomic B-C R2AC - equilibrium distance for the diatomic A-C B2AB - beta exponent for the diatomic A-B B2BC - beta exponent for the diatomic B-C B2AC - beta exponent for the diatomic A-C S2AB - Sato parameter for the diatomic A-B S2BC - Sato parameter for the diatomic B-C S2AC - Sato parameter for the diatomic A-C
A real value is expected after each one of them.
Limitations: The current implementation is only intended for a single SEVB correcting term.
Reference: A detailed description of the LEPS potential energy functionals as well as the application to an enzymatic hydride transfer can be found in,
C. Alhambra, J. Corchado, M. L. Sanchez, M. Garcia-Viloca, J. Gao & D. G. Truhlar, Journal of Physical Chemistry B, 2001, 105, 11326-11340. "Canonical Variational Theory for Enzyme Kinetics with the Protein Mean Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory and Application to Liver Alcohol Dehydrogenase."
# File: qmmm, Node: SVB, Up: Top, Previous: LEPS, Next: 2DSVB
Description of SVB command [ LEPS SVB LEPA int LEPB int LEPC int - D1AB real D1BC real D1AC real - R1AB real R1BC real R1AC reat - B1AB real B1BC real B1AC real ]
Description: A simple analytical function is included in combined QM/MM potential energy functions using semiempirical Hamiltonian for enzyme reactions to obtain more accurate energetic results. The motivation behind the simple valence bond (SVB) term is to introduce small energy corrections at critical points (reactants, transition state, and products) on the QM potential energy surface. The underlying assumption is that the general shape of the QM potential energy surface at the semiempirical level is in reasonable accord with high-level ab initio result. The SVB term is a simplified version of the semiempirical valence bond term (SEVB) invoked by the command LEPS.
The SVB term is a combination of two Morse potentials, which depend on the bond distances of the breaking and making bonds, respectively, and a coupling term that is typically (but not exclusively) a function of the donor-acceptor distance.
Specifically, for the reaction A-B + C ---> A + B-C with r1 = distance A-B r2 = distance B-C r3 = distance A-C the SVB correction along a given reaction coordinate that depends on r1 and r2 is:
VSVB = 1/2 [ M1(r1)+M2(r2) - [(M2(r2)-M1(r1))**2+4V12**2)]**1/2] where M1(r1) and M2(r2) are Morse potentials:
M1(r1) = D1AB [ exp(-2*B1AB*(r1-R1AB))-2*exp(-B1AB*(r1-R1AB)) ]
M2(r2) = D1BC [ exp(-2*B1BC*(r2-R1BC))-2*exp(-B1BC*(r1-R1BC)) ] and the coupling term has the form:
V12 = D1AC * exp(-B1AC*(r3-R1AC)) where,
D1AB = difference in dissociation energy between the reference calculation or experimental value and the dissociation energy given by semiempirical method (for the AB bond)
D1BC = difference in dissociation energy between reference calculation or experimental value and the dissociation energy given by the semiempirical method (for the BC bond)
B1AB and B1BC = related to the bond force constants (kij) and to the bond dissociation energies (D1ij) by B1ij = sqrt (kij/2*D1ij). These values can be obtained from experimentally determined frequencies or from high level calculations. R1AB, R1BC and R1AC = equilibrium bond length for bonds AB, BC, and AC, respectively.
D1AC,R1AC = adjustable parameters to obtain the desired barrier height.
Note: D1AB and D1BC may be also adjusted to obtain the desired reaction energy. The difference D1AB-D1BC is the relative correction of the product state energy respect to the reactant state energy. It is recommended to avoid negative values for these variables.
Reference: A detailed description of the SVB method as well as the application to the nucleophilic addition reaction catalized by haloalkane dehalogenase is found in:
Devi-Kesavan, L.S.; Garcia-Viloca, M.; Gao, J. Theor.Chem.Acc. 2002, in press.
Example:
...
QUANtum group sele qms end glnk sele bynu 68:69 end am1 charge 1 - scfc 0.000001 - LEPS SVB LEPA 57 LEPB 58 LEPC 13 - ! atoms involved D1AB 36.0 D1BC 15.0 D1AC 15.0 - ! energies R1AB 1.101 R1BC 1.1011 R1AC 2.707 - ! equil. bond lenghts B1AB 1.393 B1BC 1.409 B1AC 1.0 - ! exponents
...
# File: qmmm, Node: 2DSVB, Up: Top, Previous: SVB, Next: SQUANTUM
The following options allow one to construct a two-dimensional simple VB-like function to correct the (presumably) semiempirical QM/MM potential energy surface. This extends beyong the one-dimensional correction described above.
[LEPS [LEPA int LEPB int LEPC int D1AB real D1BC real D1AC real R1AB real R1BC real R1AC real B1AB real B1BC real B1AC real S1AB real S1BC real S1AC real D2AB real D2BC real D2AC real R2AB real R2BC real R2AC real B2AB real B2BC real B2AC real S2AB real S2BC real S2AC real]
[SVB [SURF] [TEST] [GCOU|G1CO|G2CO] LEPA int LEPB int [LEPC int] D1AB real D1BC real [D1AC real] R1AB real R1BC real [R1AC real] B1AB real B1BC real [B1AC real] [LEPD int LEPE int [LEPF int] D1DE real D1EF real [D1DF real] R1DE real R1EF real [R1DF real] B1DE real B1EF real [B1DF real] [VC12]]] SVB SVB turns on the Simple Valence Bond correction function. It requires correction values as difference between experimental or high-level QM level data and the semi-empirical level used. The following keywords work only with the SVB option. SURFace A two-dimensional correction term is employed TEST Additional output regarding SVB term at each energy step. Useful when testing the extent of correction needed. GCOUpling Use a gaussian coupling term which is a function of the reaction coordinate. If SURF is also switched on, this keyword will switch on gaussian terms for both coordinates. G1COuple Use gaussian coupling term for first coordinate. G2COuple Use gaussian coupling term for second coordinate. VC12 Add coupling term between two coordinates. This term is currently only a constant number.
If only two atoms are specified (LEPA and LEPB or LEPD and LEPE), a simple exponential term between the two atoms will be added. If a gaussian term is switched on via the GCOU,G1CO, or G2CO keywords, then a gaussian term will be employed instead.
# File: qmmm, Node: SQUANTUM, Up: Top, Previous: 2DSVB, Next: SQM_Syntax
********************************************************************** ****** SQUANTUM MODULE ****** Combined Quantum Mechanical and Molecular Mechanics Method Based on SQUANTM in CHARMM
The F90 semiemprical code written by Ross Walker (TSRI, AMBER) and Mike Crowley (TSRI, AMBER and CHARMM), the interface to CHARMM has been implemented by Kwangho Nam (UMN, [email protected]) including GHO and Swithing function implementation. The QM/MM-Ewald summation implementation is done as a joint project between TSRI and UMN (University of Minnesota).
The new semiempirical code, SQUANTM, is envisioned to eventually replace the current semiempirical QM code, which was originally incorporated into CHARMM by Martin Field and Paul Bash based on Stewart's MOPAC version 5 program. The SQUANTM was written in Fortran90, and the result is a substantial improvement in computational speed. However, the two packages are not in conflict as long as they are not compiled together. Therefore, all the original MOPAC-based QM/MM options and commands are kept. Should a user choose to use the SQUANTM or the MOPAC-based QM/MM algorithm, one simply follow the compiling steps highlighted below.
# File: qmmm, Node: SQM_Syntax, Up: Top, Previous: SQUANTUM, Next: SQM_Install
Syntax for SQUANTM commands
QUANtum [atom-selection] [GLNK atom-selection] [REMOve] [SWITched]
[AM1|PM3|MNDO|PDP3|PDMN] [CHARge int] [SCFCriteria real] [DOUBLET|TRIPLET]
[NEWD int] ewald-spec ewald-spec::= { [KMAX int] } [KSQMAX int] { [KMXX int] [KMXY int] [KMXZ int] }
GLNK: GHO method implementation (refer qmmm.doc).
REMOve: Classical energies within QM atoms are removed.
SWITched: Use switching function from CTONNB to CTOFNB values based on GROUp method (refer nbonds.doc). It is incompatible with NEWD options
AM1|PM3|MNDO|PDP3|PDMN: AM1 model, PM3 model, MNDO model, PDDG/PM3 (PDP3) model, and PDDG/MNDO (PDMN) model. Note: currently, GHO method only support AM1 and PM3 model. For PDDG/PM3 and PDDG/MNDO model, the reference is Repasky et al. J. Comput. Chem. (2002), 23, 1601.
NEWD and ewald-spec: refer the description for QUANTUM module.
Note: Currently, the SQUANTM module does not support UHF calculations. Thus, if you want to run UHF calculations, use QUANTUM or MNDO97 module available for CHARMM QM/MM calculations.
For QM-MM interaction, the interaction doesn't include the interaction between Gaussian core-core interactions. Thus, it is slightly different from the original implementation in QUANTUM or MNDO97 based on J. Comput. Chem. (1990) 6, 700.
# File: qmmm, Node: SQM_Install, Up: Top, Next: Top, Previous: SQM_Syntax
Installation of SQUANTM module in CHARMM
To compile SQUANTM with CHARMM, one uses: install.com [machine] [size] SQ
The "SQ" specifies to compile SQUANTM with CHARMM by replacing QUANTUM keyword in pref.dat file. Currently, the platform should support compilers that can compile F77 and F90 code simultaneously. The platform and compilers tested includ ALTIX and GNU using intel fortran compilers (ifort and efc), and IBMAIX platform using xlf90 and related compiler. CHARMM Element doc/qchem.doc $Revision: 1.3 $ # File: QChem, Node: Top, Up: (chmdoc/commands.doc), Next: Description
Combined Quantum Mechanical and Molecular Mechanics Method Based on Q-Chem in CHARMM
H. Lee Woodcock ([email protected])
based on the GAMESS(US) interface from Milan Hodoscek ([email protected],[email protected]) and the GAMESS(UK) interface from Paul Sherwood ([email protected])
Ab initio program Q-Chem is connected to CHARMM program in a QM/MM method. This method is based on the interface to the GAMESS (US version), the latter being an extension of the QUANTUM code which is described in J. Comp. Chem., Vol. 11, No. 6, 700-733 (1990).
* Menu:
* Description:: Description of the qchem commands. * Usage:: How to run Q-Chem in CHARMM. * Installation:: How to install Q-Chem in CHARMM environment. * Status:: Status of the interface code. * Functionality:: Functionality of the interface code. * RPath:: Replica Path Command * Pert:: ab inition QM/MM free energy perturbation
# File: QChem, Node: Description, Up: Top, Next: Usage, Previous: Top
The Q-Chem QM potential is initialized with the QCHEM command.
[SYNTAX QCHEm]
QCHEm [REMOve] [EXGRoup] NOGUess] (atom selection)
REMOve: Classical energies within QM atoms are removed.
EXGRoup: QM/MM Electrostatics for link host groups removed.
NOGUess: Obtains initial orbital guess from previous calculation. Default is to recalculate initial orbitals each time.
The atoms in selection will be treated as QM atoms. Link atom may be added between an QM and MM atoms with the following command:
======
ADDLinkatom link-atom-name QM-atom-spec MM-atom-spec
link-atom-name ::= a four character descriptor starting with QQ.
atom-spec::= {residue-number atom-name} { segid resid atom-name } { BYNUm atom-number }
When using link atoms to break a bond between QM and MM regions bond and angle parameters have to be added to parameter file or better use READ PARAm APPEnd command.
If define is used for selection of QM region put it after all ADDLink commands so the numbers of atoms in the selections are not changed. Link atoms are always selected as QM atoms.
======# File: QChem, Node: Usage, Up: Top, Next: Installation, Previous: Description
CHARMM input scripts are the same as before except the addition of ENVIronment commands and the QCHEm command itself. Q-Chem commands are in a separate file call qchem.inp, (or with an alternative name indicated by the "QCHEMCNT" environment variable). The Q-Chem input file has the same structure as it would have for a normal Q-Chem run, except that the specification of the geometry, in the molecule section, is omitted. Note: the charge and multiplicity are still included in the molecule section.
Names of the files for Q-Chem are specefied with environment variables as follows. These four ENVIronment variables must be set!
use ENVIronment command inside CHARMM
ENVI qchemcnt "qchem.inp" ENVI qcheminp "q1.inp" ENVI qchemexe "qchem" ENVI qchemout "qchem.out" or use the following for (t)csh
setenv qchemcnt qchem.inp setenv qcheminp q1.inp setenv qchemexe qchem setenv qchemout qchem.out or use the following for ksh,sh,bash
export qchemcnt=qchem.inp export qcheminp=q1.inp export qchemexe=qchem export qchemout=qchem.out
1. The QCHEMCNT variable specifies the main Q-Chem input file which contains the $rem section, $molecule section (without geometry), $comment section, ect..,
2. The QCHEMINP variable is the final input file that will get passed to Q-Chem. CHARMM actually writes this file and adds the correct geometry and any external/point charges (e.g. MM atoms) to an $external_charges section.
3. The QCHEMEXE is the location of the qchem script. Specify the entire path unless $QC/bin is included in your default path.
4. The QCHEMOUT file specifies the Q-Chem output file. This file get overwritten for each optimization/time step. In the future, there will be a mechanism to save old output files.
Q-Chem input file parameters ------
The following $rem variables must be specified in the QCHEMCNT file in order to perform CHARMM QM/MM or pure QM calculations. qm_mm true jobtype force symmetry off sym_ignore true print_input false qmmm_print true
1. qm_mm = true: Turns QM/MM on in Q-Chem
2. jobtype = force: Needed to do QM/MM optimizations. Set to "SP" if QM/MM energy is desired.
3. symmetry = off: Turn off symmetry
4. sym_ignore = true: Prevents Q-Chem from reorienting molecule
5. print_input = false: Use this if you have a large molecule and do not want 1000s of atoms echoed back to the output file.
6. qmmm_print = true: Reduces some of the print out during QM/MM calculations. This prevents external charges from being printed out if there are more than 50 of them.
Sample QCHEMCNT file (qchem.inp): ------$comment Input file comes from CHARMM $end
$rem exchange HF basis 6-31G* qm_mm true jobtype force symmetry off sym_ignore true print_input false qmmm_print true $end
$molecule 0 1 $end ------
The above is for 6-31G calculation of any neutral molecule.
[NOTE: For another example look at test/cquantumtest/alanine_qchem.inp]
======# File: QChem, Node: Installation, Up: Top, Next: Status, Previous: Usage
One of the main benefits of using Q-Chem to do QM/MM calculations with CHARMM is the ease of which you can get up and running jobs. All you have to do is compile CHARMM in the following way.... install.com
This will compile the serial version of CHARMM to run with a serial version of Q-Chem. To compile a parallel version of CHARMM to run with a parallel or serial version of Q-Chem you could use the following script....
------#!/bin/csh # Compile Parallel CHARMM with Q-Chem support
# USE STANDARD MPI (i.e. MPICH) setenv MPI /base/mpi/directory setenv MPI_LIB $MPI/lib setenv MPI_LIB $MPI/include
# SET THE PATH TO MPIF77 set path=($MPI/bin $path) install.com
======# File: QChem, Node: Status, Up: Top, Next: Functionality, Previous: Installation
Q-Chem/CHARMM interface status (July 2004)
- Parallel version is fully functional
- Replica/Path and Nudged Elastic Band Methods function in a highly parallel and parallel/parallel fashion (parallel/parallel is not implemented at the source code level, accomplished via CHARMM scripting).
- I/O including standard input and output are separated for Q-Chem.
- All CHARMM testcases are still OK when CHARMM is compiled with Q-Chem inside.
- QCHEM, GAMESS, GAMESSUK, CADPAC and QUANTUM keywords cannot coexist in pref.dat
- Q-Chem recognizes atoms by their masses as specified in the RTF file ======# File: QChem, Node: Functionality, Up: Top, Next: RPath, Previous: Status
1. QM/MM optimizations (analytic gradients) using Q-Chem can be performed using the following methods.
- HF* (RHF, UHF, ROHF) - DFT* (RHF, UHF, ROHF) - MP2 (RHF, UHF, ROHF) - CCSD (RHF, UHF)
* Analytic derivatives run in parallel.
2. QM/MM single point energies using Q-Chem can be performed using the following methods (in addition to the above).
Local MP2 (RHF, UHF)
3. The remainder of Q-Chem's analytic derivative and energy point methods will be made available in future releases.
======# File: QChem, Node: RPath, Up: Top, Next: Pert, Previous: Functionality
1. Additional ENVIronment variable: To do QM/MM Replica/Path or Nudged Elastic Band calculations with CHARMM and Q-Chem you must define one extra variable.
ENVI QCHEMPWD "/path/to/working/rpath/directory"
2. After defining this above ENVIronment variable all that is left to do is add the "rpath" keyword to the QCHEm call. For example...
QCHEm RPATh REMOve select qm_region end
This will create nrep directories in /path/to/working/rpath/directory and each point of the pathway will be computed in a different directory.
Note: you must be running a parallel version of CHARMM with the same number of processors as you have replicas (i.e. pathway points).
======# File: QChem, Node: Pert, Up: Top, Next: Top, Previous: RPath
To run ab initio QM/MM free energy perturbation you need to specify additional environment variables in the QM/MM setup...
1. sainp: state A control file (same as QCHEMCNT; specific for state A) 2. sbinp: state B control file (same as QCHEMCNT; specific for state B) 3. stateainp: auto generated Q-Chem input file for state A 4. statebinp: auto generated Q-Chem input file for state B 5. stateaout: specify Q-Chem output for state A QM calculation 6. statebout: specify Q-Chem output for state B QM calculation Example...
envi qchemexe "qchem" ! Command to call quantum program envi qchemcnt "data/qchem_pert.inp" ! Non Pert Control file envi qcheminp "q1.inp" ! Non Pert Quantum input file envi qchemout "qchem.out" ! Non Pert Quantum output file envi sainp "data/s0.inp" ! State 0 control file envi sbinp "data/s1.inp" ! State 1 control file envi stateainp "state0.inp" ! State 0 quantum input file envi statebinp "state1.inp" ! State 1 quantum input file envi stateaout "state0.out" ! State 0 quantum output file envi statebout "state1.out" ! State 1 quantum output file
See test/cquantumtest/qmmm_pert.inp for a complete example.
Please see pert.doc for a complete description of running free energy perturbation in CHARMM.
======CHARMM Element doc/gamess.doc 1.1 # File: Gamess, Node: Top, Up: (chmdoc/commands.doc), Next: Description
Combined Quantum Mechanical and Molecular Mechanics Method Based on GAMESS in CHARMM
by Milan Hodoscek ([email protected],[email protected])
Ab initio program GAMESS (General Atomic and Molecular Electronic Structure System) is connected to CHARMM program in a QM/MM method. This method is extension of the QUANTUM code which is described in J. Comp. Chem., Vol. 11, No. 6, 700-733 (1990).
* Menu:
* Description:: Description of the gamess commands. * Using:: How to run GAMESS in CHARMM. * Replica path:: How to run GAMESS/CHARMM with REPLICA/PATH. * Installation:: How to install GAMESS in CHARMM environment. * Status:: Status of the interface code. * Functionality:: Functionality of the interface code. * Implementation:: Implementation. # File: Gamess, Node: Description, Up: Top, Next: Usage, Previous: Top
The GAMESS QM potential is initialized with the GAMEss command.
[SYNTAX GAMEss]
GAMEss [REMOve] [EXGRoup] [QINPut] [BLURred] [NOGUess] [FMO] (atom selection)
REMOve: Classical energies within QM atoms are removed.
EXGRoup: QM/MM Electrostatics for link host groups removed.
QINPut: Charges are taken from PSF for the QM atoms. Charges may be non integer numbers. Use this with the REMOve!
NOGUess: Obtains initial orbital guess from previous calculation. Default is to recalculate initial orbitals each time.
FMO: Enable Fragment MO method with CHARMM
BLURred: MM charges are scaled by a gaussian function (equivalent to ECP) Width of the gaussian function is specified in WMAIN array (usually by SCALar command) The value for charge is taken from PSF. Some values of WMAIN have special meaning:
WMAIN.GT.999.0 ignore this atom from the QM/MM interaction WMAIN.EQ. 0.0 treat this atom as point charge in the QM/MM potential
The atoms in selection will be treated as QM atoms. Link atom may be added between an QM and MM atoms with the following command:
ADDLinkatom link-atom-name QM-atom-spec MM-atom-spec
link-atom-name ::= a four character descriptor starting with QQ.
atom-spec::= {residue-number atom-name} { segid resid atom-name } { BYNUm atom-number }
When using link atoms to break a bond between QM and MM regions bond and angle parameters have to be added to parameter file or better use READ PARAm APPEnd command. Also note that QQH type has to be added in the RTF file (see test/c25test/gmstst.inp).
If define is used for selection of QM region put it after all ADDLink commands so the numbers of atoms in the selections are not changed. Link atoms are always selected as QM atoms.
======# File: Gamess, Node: Usage, Up: Top, Next: Replica Path , Previous: Description
In order to run GAMESS and CHARMM on parallel machines I/O of GAMESS and CHARMM was separated. This is now true even for scalar runs. CHARMM input scripts are the same as before except the addition of ENVIronment commands and GAMEss command itself. GAMESS commands are in a separate file which is pointed to by INPUT environment variable.
Names of the files for GAMESS are specefied with environment variables as follows:
use ENVIronment command inside CHARMM
envi INPUT "test.gms" ! quotes needed for lowercase names envi OUTPUT "test.out" envi PUNCH "scratch/test.dat" envi DICTNRY "scratch/test.F10" envi WORK15 "scratch/test.F15" envi DASORT "scratch/test.F20"
or use (t)csh
setenv INPUT test.gms setenv OUTPUT test.out setenv PUNCH scratch/test.dat setenv DICTNRY scratch/test.F10 setenv WORK15 scratch/test.F15 setenv DASORT scratch/test.F20
or ksh,sh,bash
export INPUT = test.gms export OUTPUT = test.out export PUNCH = scratch/test.dat export DICTNRY = scratch/test.F10 export WORK15 = scratch/test.F15 export DASORT = scratch/test.F20
For complete information about GAMESS input see INPUT.DOC file in GAMESS distribution. (NIH: ~milan/gamess/hp/INPUT.DOC)
Example: ------
GAMESS commands have to be in a separate file. Example for the GAMESS input follows:
------$CONTRL COORD=CART NOSYM=1 NPRINT=-5 ! This is rarely changed SCFTYP=RHF ICHARG=0 ! This usually has to be changed RunTyp=Gradient ! Normally forces are needed ! RunTyp=Energy ! If only energy is needed $END $SYSTEM MEMORY=1000000 ! memory allocation TIMLIM=100000 $END $BASIS GBASIS=N31 NGAUSS=6 $END $SCF DIRSCF=.True. $END ! DIRSCF=.true. recommended ! if there are convergence problems ! try SOSCF=.FALSE. $DATA ! This can be empty
$END ------
The above is for 6-31G calculation of any neutral molecule. $DATA section may be left empty or filled with basis set information in the case when it cannot be specified by the $BASIS keyword.
[NOTE: For more examples look at test/c25test/gmstst.inp]
======
# File: Gamess, Node: Replica Path, Up: Top, Next: Installation, Previous: Usage
Replica/Path method (parallel/parallel setup) ------
Running GAMESS/CHARMM interface with Replica/Path method needs few additional steps:
- GAMESS/CHARMM must be compiled with the parallel functionality. Make sure that the GENCOMM keyword is in pref.dat. (Run CHARMM interactively and type pref).
- The number of processes must be equal to number of replicas multiplied by an integer (1,2,3...). This ensures that each replica is an independent process. If the factor is more than 1, it means each replica will run itself in parallel (parallel/parallel). - GAMESS control file (the one assigned to the INPUT environment variable) must be linked the number of replica times. Each symbolic link must have _
- The path to the above link must be absolute. This depends on the way CHARMM is run in parallel. For example for MPICH library on must use the following command:
charmm -p4wd /data/rpath/reaction -p4pg 20cpus < inp > out
The /data/rpath/reaction must be the same on all the processes, either exact copies or NFS mounted.
- The gamess output files have also _
# File: Gamess, Node: Installation, Up: Top, Next: Status, Previous: Replica Path
Installation ------
Look at the GAMESS home page for instructions how to obtain the code.
Installation itself cannot be automated yet so one has to follow this procedure (if there are any problems ask [email protected]):
1. Put all the source (*.src and *.c) files in source/gamint/gamess
2. Follow instructions in the begining of the gamess.src file, to change: C C ----- CHARMM INTERFACE ----- C TO USE GAMESS FROM INSIDE OF CHARMM, YOU MUST C 1. INITIALIZE KCHRMM JUST BELOW TO 1 C 2. CHANGE "PROGRAM GAMESS" ABOVE TO "SUBROUTINE GAMESS" C 3. CHANGE THE "STOP" STATEMENT BELOW TO "RETURN" C 4. DELETE DUMMY SUBROUTINES -CHGMIU- AND -CHMDAT- BELOW C 5. CHANGE -MXCHRM- FROM 1 TO 25120 IN ALL PARAMETER DEFINITIONS C FOUND IN GAMESS,GRD1,INPUTB,INPUTC,INT1 MODULES
3. install.com
The compile scripts are available for the following platforms:
T3E, T3D, IBMRS, IBM/SP, SUN, SGI, HP-UX, Convex SPP, DEC alpha, PC/Linux with 3 compilers (Absoft, f2c, g77)
======
# File: Gamess, Node: Status, Up: Top, Next: Functionality, Previous: Installation GAMESS/CHARMM interface status (July 1996)
- Parallel version is fully functional
- I/O including standard input and output are separated for GAMESS.
- All CHARMM testcases are still OK when CHARMM is compiled with GAMESS inside.
- GAMESS, CADPAC and QUANTUM keywords cannot coexist in pref.dat
- MNDO, AM1, PM3 hamiltonians work only in pure QM calculations. No QM/MM energies and derivatives with this wavefunctions yet.
- GAMESS recognizes atoms by their masses as specified in the RTF file
# File: Gamess, Node: Functionality, Up: Top, Next: Implementation, Previous: Status
The following methods work with the GAMESS/CHARMM (from GAMESS INTRO.DOC file)
I. A wide range of quantum chemical computations are possible using GAMESS in the CHARMM MM field, which
1. Calculates RHF, UHF, ROHF, GVB, or MCSCF self- consistent field molecular wavefunctions.
2. Calculates CI or MP2 corrections to the energy of these SCF functions.
3. Calculates analytic energy gradients for all SCF wavefunctions, plus closed shell MP2 or CI.
4. Optimizes molecular geometries using the energy gradient, in terms of Cartesian or internal coords.
5. Searches for potential energy surface saddle points.
6. Computes the energy hessian, and thus normal modes, vibrational frequencies, and IR intensities.
7. Traces the intrinsic reaction path from a saddle point to reactants or products.
8. Traces gradient extremal curves, which may lead from one stationary point such as a minimum to another, which might be a saddle point.
9. Follows the dynamic reaction coordinate, a classical mechanics trajectory on the potential energy surface.
10. Computes radiative transition probabilities. 11. Evaluates spin-orbit coupled wavefunctions.
12. Applies finite electric fields, extracting the molecule's linear polarizability, and first and second order hyperpolarizabilities.
13. Evaluates analytic frequency dependent non-linear optical polarizability properties, for RHF functions.
14. Obtains localized orbitals by the Foster-Boys, Edmiston-Ruedenberg, or Pipek-Mezey methods, with optional SCF or MP2 energy analysis of the LMOs.
15. Calculates the following molecular properties: a. dipole, quadrupole, and octupole moments b. electrostatic potential c. electric field and electric field gradients d. electron density and spin density e. Mulliken and Lowdin population analysis f. virial theorem and energy components g. Stone's distributed multipole analysis
16. Models solvent effects by a. effective fragment potentials (EFP) b. polarizable continuum model (PCM) c. self-consistent reaction field (SCRF)
II. A quick summary of the current program capabilities is given below.
SCFTYP= RHF ROHF UHF GVB MCSCF ------Energy CDP CDP CDP CDP CDP
analytic gradient CDP CDP CDP CDP CDP
numerical Hessian CDP CDP CDP CDP CDP
analytic Hessian CDP CDP - CDP -
MP2 energy CDP CDP CDP - C
MP2 gradient CD - - - -
CI energy CDP CDP - CDP CDP
CI gradient CD - - - -
MOPAC energy yes yes yes yes -
MOPAC gradient yes yes yes - -
C= conventional storage of AO integrals on disk D= direct evaluation of AO integrals P= parallel execution III. The methods listed above which don't have analytic gradients are not available for CHARMM minimizations and dynamic calculations.
IV. The following are available only in the pure QM calculations:
1. Calculates semi-empirical MNDO, AM1, or PM3 RHF, UHF, or ROHF wavefunctions.
# File: Gamess, Node: Implementation, Up: Top, Next: Top, Previous: Functionality
Implementation ------
This is for version 27 JUN 2005 R3 (from Dec 10, 2005) of GAMESS or later:
The DDI (Distributed Data Interface) library is used by parallel GAMESS. Normally GAMESS uses the simplified emulation of the full DDI library implemented in the CHARMM interface (source/gamint/ddi.src). However some of the methods (like parallel MP2) require the original version of DDI, which can be used by specifying DDIMPI keyword in the pref.dat file. Also the libddi.a from GAMESS distribution has to be put to build/gnu/mpi directory.
The following files need to be removed from gamint/gamess directory: vector.src
The following files are modified from original GAMESS:
gamint/gamess/gamess.src gamint/gamess/grd1.src gamint/gamess/grd2a.src gamint/gamess/guess.src gamint/gamess/inputa.src gamint/gamess/inputb.src gamint/gamess/inputc.src gamint/gamess/int1.src gamint/gamess/iolib.src gamint/gamess/mccas.src gamint/gamess/prpel.src gamint/gamess/prppop.src gamint/gamess/prplib.src gamint/gamess/rhfuhf.src gamint/gamess/scflib.src gamint/gamess/unport.c gamint/gamess/zunix.c
Some changes for CHARMM interface into upstream version of the GAMESS still didn't made it so contact [email protected] for more info. CHARMM Element doc/gamessuk.doc 1.1 # File: GamessUK, Node: Top, Up: (chmdoc/commands.doc), Next: Description
Combined Quantum Mechanical and Molecular Mechanics Method Based on GAMESS-UK in CHARMM
Paul Sherwood ([email protected])
based on the GAMESS(US) interface from Milan Hodoscek ([email protected],[email protected])
Ab initio program GAMESS-UK (General Atomic and Molecular Electronic Structure System, UK version) is connected to CHARMM program in a QM/MM method. This method is based on the interface to the GAMESS (US version), the latter being an extension of the QUANTUM code which is described in J. Comp. Chem., Vol. 11, No. 6, 700-733 (1990).
* Menu:
* Description:: Description of the gamess commands. * Using:: How to run GAMESS in CHARMM. * Installation:: How to install GAMESS in CHARMM environment. * Status:: Status of the interface code.
# File: GamessUK, Node: Description, Up: Top, Next: Usage, Previous: Top
The GAMESS QM potential is initialized with the GAMEss command.
[SYNTAX GAMEss]
GAMEss [REMOve] [EXGRoup] [QINPut] [BLURred] (atom selection)
REMOve: Classical energies within QM atoms are removed.
EXGRoup: QM/MM Electrostatics for link host groups removed.
QINPut: Charges are taken from PSF for the QM atoms. Charges may be non integer numbers. Use this with the REMOve!
BLURred: MM charges are scaled by a gaussian function (equivalent to ECP) Width of the gaussian function is specified in WMAIN array (usually by SCALar command) The value for charge is taken from PSF. Some values of WMAIN have special meaning:
WMAIN.GT.999.0 ignore this atom from the QM/MM interaction WMAIN.EQ. 0.0 treat this atom as point charge in the QM/MM potential
The atoms in selection will be treated as QM atoms.
Link atom may be added between an QM and MM atoms with the following command:
ADDLinkatom link-atom-name QM-atom-spec MM-atom-spec link-atom-name ::= a four character descriptor starting with QQ.
atom-spec::= {residue-number atom-name} { segid resid atom-name } { BYNUm atom-number }
When using link atoms to break a bond between QM and MM regions bond and angle parameters have to be added to parameter file or better use READ PARAm APPEnd command.
If define is used for selection of QM region put it after all ADDLink commands so the numbers of atoms in the selections are not changed. Link atoms are always selected as QM atoms.
======# File: GamessUK, Node: Usage, Up: Top, Next: Installation , Previous: Description
CHARMM input scripts are the same as before except the addition of ENVIronment commands and the GAMEss command itself. GAMESS-UK commands are in a separate file call gamess.in, (or with an alternative name indicated by the "gamess.in" environment variable. The GAMESS-UK input file has the same structure as it would have for a normal GAMESS-UK run, except that the specification of the geometry is omitted.
Names of the files for GAMESS-UK are specefied with environment variables as follows. It is essential to provide a routing for ed3 to ensure it is available to hold information between GAMESS-UK calls, other file specifications are optional.
use ENVIronment command inside CHARMM
envi "ed2" "/scratch/user/test.ed2" ! quotes needed for lowercase names envi "ed3" "/scratch/user/test.ed3"
or use (t)csh
setenv ed2 /scratch/user/test.ed2 setenv ed3 /scratch/user/test.ed3
or ksh,sh,bash
export ed2=test.ed2 export ed3=test.ed3
or within GAMESS-UK, use the file predirective file ed3 /scratch/user/test.ed3 file ed2 /scratch/user/test.ed2
You can use the "gamess.out" environment variable to control the routing of the GAMESS-UK output, or you can define it as stdout as follows (csh version):
setenv gamess.out stdout in which case the GAMESS-UK output will be mixed with the charmm output. (Note these don't seem to work with the bash shell, as the export command doesn't accept variable names containing a period (.), we will have to change this part of the code. GAMESS-UK input file directives ------
The GAMESS-UK data is provided in a separate file, which follows GAMESS-UK format except that there is no coordinates section.
In addition to those directives needed to switch on the reuiqred energy expresion, you should
1) include "runtype gradient" to force the computation of both energy and forces (unless you are sure you are not going to invoke any calculation that requires a gradient from your script).
2)It is advised that the GAMESS-UK directives
noprint dist anal
be included as these diagnostic calculations don't contribute to the charmm job but use a lot of memory when there are a lot of classical atoms.
3) Make sure the gamess input contains a generous time card, since the GAMESS calculation will be skipped if it thinks it has run out of time.
4) If you see that the quantum part of the energy goes to zero, it may reflect the timeout condition above, or some other non-fatal problem in GAMESS-UK. Check the GAMESS-UK log file.
5) The directive "chm" may be added to set CHARMM-specific options as follows:
chm noatom : request that GAMESS-UK output items that list all the atoms be suppressed This is important for macromolecular systems.
chm append : request that all outputs be concatenated (the default is that you will only save the last one)
chm offset : provide an energy offset to be added to all the QM energies. This can help ensure the values print within the fields expected in CHARMM.
chm debug : diagnostic print (not recommended unless developing) Example: ------
GAMESS commands have to be in a separate file. Example for the GAMESS input follows:
------core 5000000 chm append chm noatompr chm offset 100 title qm region for charmm charge 0 adapt off nosym noprint distance analysis basis 6-31g scftype rhf runtype gradient vectors atoms enter 1
The above is for 6-31G calculation of any neutral molecule.
[NOTE: For more examples look at test/c28test/cquantumtest/]
For complete information about GAMESS input see the CFS web site http://www.dl.ac.uk/CFS.
For further information and updates on CHARMM/GAMESS-UK interface see http://www.cse.clrc.ac.uk/qcg/chmguk
======
# File: GamessUK, Node: Installation, Up: Top, Next: Status, Previous: Usage
Installation ------
Installation itself cannot be fully automated yet so one has to follow this procedure (if there are any problems ask [email protected]):
1. Unpack the GAMESS-UK distribution as a subdirectory of gukint: source/gukint/GAMESS-UK
2. install.com
The build procedure works by executing a configuration script within the GAMESS-UK source tree, (GAMESS-UK/utilities/charmm_configure). Assuming GAMESS-UK has not already been ported to the target platform, it is this file that will generally need modification on plaforms for which the CHARMM/GAMESS-UK interface has not been tested. The following is a summary of the status (c28 release)
Architecture CHARMM host Parallel Status keyword Options
SGI R4400 sgi - OK Pentium/Linux gnu - OK gnu mpich OK Compaq alpha - OK
Porting Notes ------
It is necessary to ensure that charmm_configure processes the GAMESS-UK Makefiles with a valid set of keywords, the most important on being the machine type. Unfortunately there isn't a one-to-one mapping between CHARMM host types and GAMESS-UK machine types which complicates the charmm_configure script.
Similarly, changes to charmm_configure may be needed to request the required GAMESS-UK configuration options for a parallel build. Probably the best bet for a simple parallel GAMESS-UK/CHARMM code is to select MPI with static load balancing options, for which the "mpi" keyword needs to be passed to configure.
On some platforms the Global Array port of GAMESS-UK can be used, but this is not supported yet by the standard distribution. See the web site http://www.cse.clrc.ac.uk/Activity/CHMGMS for more details of the current status.
NB The GAMESS-UK distribution can only support a single architecture (there are no architecture dependent directories). When moving the code from one platform to another, be sure to clear out the object and library files
% cd source/gukint/GAMESS-UK/m4 % make clean
When building the parallel code the additional, manual steps will be needed
For the MPI code
- in install.com, set the environment variables MPI_LIB - the directory holding libmpi.a (or similar) MPI_INCLUDE - the directory holding mpif.h (etc)
you may also need to edit GAMESS-UK/m4/Makefile.in as these directories are specified for most platforms.
- Some changes may be needed to build/UNX/Makefile_
======# File: GamessUK, Node: Status, Up: Top, Next: Top, Previous: Installation
GAMESS-UK/CHARMM interface status (July 2000)
- Parallel version is functional, but for most platforms it will require changes to install.com Makefile_$chmhost and/or charmm_configure to activate
- All CHARMM testcases are still OK when CHARMM is compiled with GAMESS-UK inside.
- GAMESS, GAMESSUK, CADPAC and QUANTUM keywords cannot coexist in pref.dat
- GAMESS-UK recognizes atoms by their masses as specified in the RTF file CHARMM Element doc/sccdftb.doc $Revision: 1.4 $ # File: SCCDFTB, Node: Top, Up: (chmdoc/commands.doc), Next: Description
Combined Quantum Mechanical and Molecular Mechanics Method Based on SCCDFTB in CHARMM
by Qiang Cui and Marcus Elstner ([email protected], [email protected])
The approximate Density Functional program SCCDFTB (Self-consistent charge Density-Functional Tight-Binding) is interfaced with CHARMM program in a QM/MM method.
This method is described in
Phys. Rev. B 58 (1998) 7260, Phys. Stat. Sol. B 217 (2000) 357, J. Phys. : Condens. Matter. 14 (2002) 3015.
The QM/MM interface in CHARMM has been described in J. Phys. Chem. B 105 (2001) 569
The GHO-SCC-DFTB/MM boundary treatment has been described in J. Phys. Chem. A 108 (2004) 5454.
* Menu:
* Description:: Description of the sccdftb commands. * Usage:: How to run sccdftb in CHARMM. * Installation:: How to install sccdftb in CHARMM environment. * Status:: Status of the interface code.
# File: SCCDFTB Node: Description, Up: Top, Next: Usage, Previous: Top
The SCCDFTB QM potential is initialized with the SCCDFTB command
[SYNTAX SCCDFTB]
SCCDFTB [REMOve] [CHRG] (atom selection) [GLNK atom-selection] [TEMPerature] [SCFtolerance] [CUTF] [EWAD EOPT KAPPA kappa KMAX kmax KSQMAX ksqmax] [UPDT 0] [MULL] [DISP] [HBON GAUS] [DHUB DHGA]
REMOve: Classical energies within QM atoms are removed.
CHRG: Net charge in the QM subsystem.
The atoms in selection will be treated as QM atoms.
GLNK atom-selection: contains a list of atoms that are selected as GHO boundary atoms.
TEMPerature: Specifies the electronic temperature (Fermi distribution). Can be used to accelerate or achieve SCF convergence (default =0.0).
SCFtolerance: Convergence criteria for the SCF cycle. As default a value of 1.d-7 is used.
CUTF: a flag that turns on cut-off, will use the same scheme used for MM interactions (allows atom-based fshift and fswitch)
EWAD: a flag that turns on ewald summation for QM-QM and QM-MM electrostatic interactions EOPT: performs an internal optimization for kappa and kmax as well as real-space sum. NOT recommended - very inefficient. incompatible with CUTF
KAPPA, KMAX, KSQMAX: parameters used for QM-QM and QM-MM ewald contributions.
UPDT: Whether to update the box during a MD run. Default is 0 (not update!) Do NOT forget to specify this to 1 when running CPT calculations
MULL: Transfer the mulliken charges to the CG array such that they can be printed out by transferring the CG array to any vectors (e.g., scalar wmain = charge; print coor)
DISP: Dispersion interactions among QM atoms can be calculated using an empirical formular (Elstner et al. J. Chem. Phys. 114, 5149, 2001). One needs to specify a set of parameters in the DISPERSION.INP file (see the above ref for details).
HBON: The short-range behavior of XH gamma function is modified with a damping function. This significantly enhances the hydrogen bonding interactions (Elstner, Cui, unpublished). The dampling exponent needs to be specified in the sccdftb.dat file. However, with the modified gamma, the repulsive potential has to be adjusted accordingly. This can be done in an empirical fashion by including a Gaussian (constrained to operate in a range by a switching function) in the relevant repulsive potential; the parameters for the Gaussian and the switching function need to be specified in the spl file and turned on using the GAUS keyword.
DHBU: To improve proton affinities, which depend much on the charges in the protonated DHGA and deprotonated molecules, the SCC-DFTB is expanded to the 3rd order. Currently only on-site terms have been included, which were observed to have a major impact on the calculated PAs for many molecules. The relevant parameters are the derivative of the Hubbard parameters (related to chemical hardness), which need to be specified in the sccdftb.dat file. The DHGA keyword includes further flexibility in the behavior of the Hubbard parameters as a function of charge (Elstner, Cui, unpublished).
In the SCCDFTB program the atomtypes are represented by consecutive numbers. The definition of SCCDFTB atom numbers has to be accomplished before invoking the SCCDFTB command. The numbers are stored in WMAIN. If the QM system e.g contains only O, N, C and H atoms, the the numbering can be executed as follows: scalar WMAIN set 1.0 sele type O* SHOW end scalar WMAIN set 2.0 sele type N* SHOW end scalar WMAIN set 3.0 sele type C* SHOW end scalar WMAIN set 4.0 sele type H* SHOW end
Now, the O atoms are represented by 1.0, the N atoms by 2.0 etc.
Link atom may be added between an QM and MM atoms with the following command:
ADDLinkatom link-atom-name QM-atom-spec MM-atom-spec
link-atom-name ::= a four character descriptor starting with QQ.
atom-spec::= {residue-number atom-name} { segid resid atom-name } { BYNUm atom-number }
When using link atoms to break a bond between QM and MM regions bond and angle parameters have to be added to parameter file or better use READ PARAm APPEnd command.
If define is used for selection of QM region put it after all ADDLink commands so the numbers of atoms in the selections are not changed. Link atoms are always selected as QM atoms.
# File: SCCDFTB Node: Usage, Up: Top, Next: Installation, Previous: Description
SCCDFTB input files ------
SCCDFTB needs to read in the parameter files, which have a two-body character. Therefore, the interaction parmeters for all pairs of atoms have to be read in. These files are named like oo.spl, on.spl, oc.spl, no.spl etc., where oo.spl contains the two-center integrals for the O-O interaction, on.spl the two-center integrals for the O-N interaction etc. DFTB needs these parameters for the O-N and N-O interaction, similarily for all other pairwise interactions. The file sccdftb.dat contains the paths to these parameters, as:
'potential:atom-1-atom-1' 'potential:atom-1-atom-2' 'potential:atom-1-atom-3' ... \\ 'potential:atom-1-atom-N' 'potential:atom-2-atom-1' ... \\ 'potential:atom-2-atom-N' 'potential:atom-N-atom-1' ... \\ 'potential:atom-N-atom-N' where atom-1 is the atom defined by 1.0, as described above, atom-2 defined in WMAIN by 2.0 etc.
For the example of the system containing O N C and H, sccdftb.dat would contain: 'PATH/oo.spl' 'PATH/on.spl' 'PATH/oc.spl' 'PATH/oh.spl' 'PATH/no.spl' 'PATH/nn.spl' 'PATH/nc.spl' 'PATH/nh.spl' 'PATH/co.spl' 'PATH/cn.spl' 'PATH/cc.spl' 'PATH/ch.spl' 'PATH/ho.spl' 'PATH/hn.spl' 'PATH/hc.spl' 'PATH/hh.spl' where PATH specifies the path to the directory where the data files are located. Be careful, an error in the sequence or a wrong assingnment of parameters to atoms (coordinates) will make results meaningless. Parameter files can be requested from Marcus Elstner ([email protected]).
SCCDFTB output files (currently disabled) ------
SPE.DAT : contains the Kohn-Sham energies with occupations numbers. CHR.DAT : contains the atomic (Mulliken) charges of the atoms (first row) and for the orbitals (s, px,py,pz,dxx.. ) in the following columns. REST.DAT: contains dipolemoment (D), calculated from the Mulliken charges (not a reliable estimate of Dipolemoment in general!)
# File: SCCDFTB Node: Installation, Up: Top, Next: Status, Previous: Usage
Installation of SCCDFTB ------
The source code of SCCDFTB ist distributed with CHARMM. To compile the SCCDFTB method as the quantum part: ./install machine size T T invokes the SCCDFTB The parameter files have to be reqeusted and stored in a directory, which can be reached by 'PATH' (see up).
Diagonalization routines ------
As default, the library routine dsygv.f (LAPACK) is used for the diagonalization of the hamiltonian matrix. This is called by chmdir/source/scctbint/scctbsrc/ewevge.f. A faster (about factor 2) solution is given by the dsygvd.f routine (but less stable), which is called by ewevge-dsygvd.f: copy ewevge-dsygvd.f to ewevge.f and recompile to invoke this option. Contact Marcus Elstner for more details or questions. File: SCCDFTB Node: FEP , Up: Top, Next: Top, Previous: Installation
Free energy perturbations with SCC-DFTB/MM
The code currently allows dual-topology based SCC-DFTB/MM free energy perturbation calculations; since all scaling related to the QM component of the free energy derivative is done inside SCC-DFTB, the FEP calculations do not have to use BLOCK.
As discussed in JPC, 107, 8643 (2003), a practical problem of using FEP with QM/MM potentials is that the structure of the QM region undergoes significant distortions at end-points if one scales the entire QM molecule; there is no such problem if one chooses to scale only QM/MM interactions, but that requires calculation of new terms. The general solution is to add harmonic constraints on the QM part - either only at the end-points and then re-weight the calculated free energy derivatives - or, more elegantly, add harmonic constraints as "chaperones" throughout the "alchemy" simulation and compute corrections based on local configuration integrals. See W. Yang et al. J. Chem. Phys. 2004.
For the special case where the two end-states have very similar chemical structures - such as in redox, metal-exchange and pKa applications, which we believe are scenarios where QM/MM treatment is useful, a simple dual-topology-single-coordinate (DTSC) approach has been introduced. As the name implies, one uses only one set of coordinates for the two states (e.g., reduced and oxidized states). Due to the fact that the free energy is path-independent, such an approach is formally exact. In practical applications, error might arise due to SHAKE - i.e. X-H distances are assumed to the same in the two states - which usually has negligible effects.
At each configuration (hence single-coordinate) along the trajectory, two electronic structure calculations are carried out (dual topology) and the free energy derivative with respect to the coupling parameter is evaluated and averaged on the fly.
With minor modifications, the algorithm also works for pKa prediction for a specific group in large molecules. For more details, refer to the following publications:
M. Formaneck, G. Li, X. Zhang, Q. Cui, J. Thero. Comput. Chem. 1, 53-68 (2002) G. Li, X. Zhang, Q. Cui, J. Phys. Chem. B (2003) 107, 8643 G. Li, Q. Cui, J. Phys. Chem. B, (2003) 107, 14521
NOTE BENE: It MUST be used with "FAST OFF" because only generic atom-atom codes have been modified so far (made default).
Due to the fact that ALL QM related components are handled within SCC (including GSBP and eWald, see next section), FEP (such as pKa) calculations can be used with both eWald and GSBP - provided that it is the QM part that undergoes "alchemical" mutation. The code has NOT been extensively tested in which both QM and MM undergo changes.
Two examples are given to illustrate computational details; the first one deals with redox potential calculations for FAD in Cholesterol oxidase, and the second one concerns pKa calculations of ethanethiol (Ch3CH2SH) in water. The test files are scc_fep_dtsc.inp and scc_pka1/2.inp. Example(1) ------For redox potential calculations, the following set-up is used, ......
SCCDFTB LAMDa [REST] STOP [CUTF] OUTPut int - [REMOve] (atom selection 1) [CHRG] [TEMPerature] [SCFtolerance] - INIT @lam PASS int STEP int TIAV int - [CHRG] [TEMPerature] [SCFtolerance] - (atom selection 2) - (atom selection 3)
LAMD: invoke the TI method to perform free energy calculations REST: Restart option for accumulating statistics concerning
For pKa calculations, two free energy simulations are in principle required; in the first step, the protonated state is mutated into the ionized state as the acidic proton is mutated into a dummy atom in the second step, the dummy atom is transferred into the gas phase. Test calculations indicate that the contribution from the 2nd step is likely to be small.
Example(2a) ------In the first step, BLOCK is used together with SCCDFTB ......
BLOCK 3 SCCDFTB STOP PKAC ISTP 1 CALL 2 SELE qm1 END CALL 3 SELE qmh END CALL 1 SELE .not. (qm1 .or. qmh) END COEF 1 1 1.0 COEF 1 2 1.0 COEF 1 3 1.0 COEF 2 2 0.0 COEF 2 3 @lam COEF 3 3 0.0 END
SCCDFTB PKAC ISTP 1 HYGN int [CUTF] OUTPut int - [REMOve] (atom selection 1) [CHRG] [TEMPerature] [SCFtolerance] - INIT @lam PASS int STEP int TIAV int - [CHRG] [TEMPerature] [SCFtolerance] - atom selection 2 - atom selection 3 ......
In the BLOCK section : the SCCD keyword is used to set up coefficent matrix for calculating bonded contribution involving the dummy atom to
In the SCCDFTB section: PKAC : invoke pKa calculation ISTP 1: the first step in pKa calculations HYGN : atomic index (number) of the acidic proton in the psf atom selection 1: protonated state (CHRG: protonated state) atom selection 2: protonated state (CHRG: deprotonated state) atom selection 3: deprotonated state
Example(2b) ------In the second step for pKa calculations, the dummy atom is transferred into vacuum,
...... calc 1mlam 1.0-@lam
BLOCK 3 SCCDFTB STOP PKAC ISTP 2 CALL 2 SELE qm1 END CALL 3 SELE qmh END CALL 1 SELE .not. (qm1 .or. qmh) END COEF 1 1 1.0 COEF 1 2 1.0 COEF 1 3 @1mlam COEF 2 2 0.0 COEF 2 3 0.0 bond 1.0 angl 1.0 dihe 1.0 COEF 3 3 0.0 END
SCCDFTB PKAC ISTP 2 HYGN int [CUTF] OUTPut int - [REMOve] [CHRG] (atom selection 1) [TEMPerature] [SCFtolerance] - INIT @lam PASS int STEP int TIAV int ......
Note that with BLOCK, the coefficient matrix is different in the second step: we are only scaling the non-bond (vdW) interaction between the environment and the dummy atom (1 and 3). The bonded terms between the QM and the dummy atom (2 and 3) is kept (coefficient as 1.0) and will be taken out with local configuration integrals.
In SCC-DFTB, atom selection 1: deprotonated state
File: SCCDFTB Node: Electrostatics, Up: Top, Next: Status, Previous: FEP
Since 2004, electrostatics in SCC-DFTB/MM simulations can be treated in several ways for both spherical and periodic conditions: i). As for other QM packages, the default is no cut-off for QM/MM electrostatic interactions. This is NOT recommended when cut-off is used for MM; the imbalance will cause over-polarization of the media (e.g.,see discussion in classical simulations by Woods, J. Chem. Phys. 103, 6177, 1995). A useful option is to use extended electrostatics for MM. ii). Cut-off is introduced for QM/MM electrostatics, similar to MM interactions; i.e., the same scaling factors are the same as those for MM interactions. Simply add "CUTF" to the SCC-DFTB command line. Currently only supports energy/force- shifts based on atoms iii). For spherical boundary conditions, the GSBP approach can now be used with SCC-DFTB. The current implementation takes GSBP contributions into the SCF iteration, although for a large inner region, this may not be necessary. Further tests are being carried out. The code will be extended to other boundary conditions and QM methods in the future. If one uses sorting (i.e., truncate size of basis in GSBP), make sure a SCC-DFTB/MM energy calculation with MULL (save Mulliken charge) is carried out before issuing GSBP, since the Mulliken charges are used to estimate contributions from various basis functions to the QM related terms. See test cases for examples. iv). For PBC simulations, one can use either cut-off or eWald sum for SCC-DFTB/MM interactions. No PME has been implemented for the QM/MM interactions although it may not be too unreasonable to use PME for the expensive MM part and ewald for QM/MM interactions. The current QM/MM implementation allows in principle all cell shapes. For eWald, one can either let the code optimize the exponent to get the best balance between real space sum and the reciprocal space sum (EOPT) or one can specify a set of parameters (Kappa, KMAX, KSQMAX). The real space sum is done till convergence is met with EOPT or without CUTF (so more expensive); EOPT is incompatible with CUTF. With cutoff (CUTF), the real sum is limited to atoms within the cutoff- which is recommended (much more efficient). In any case, one should carefully test kappa, KMAX to ensure the convergence of energy and, more importantly, force from SCC-DFTB/MM calculations.
A sample command line would be: ...... SCCDFTB remove CHRG 2 SELE resn @m END TEMP 0.00 SCFT 0.00000001 EWAD - CUTF Kappa 0.45 KMAX 6 KSQMAX 100 ......
The eWald code is not as efficient as one might hope for at this stage. Typically QM/MM-eWald is about 5-8 times slower than a QM/MM calculation without eWald.
An important point for PBC simulations is that all image must be used with "UPDAte IMAL ". This is because symmetry operations have not been considered in the SCC-DFTB/MM code - which obviously needs to be fixed in the future.
File: SCCDFTB Node: Status, Up: Top, Next: GLNK, Previous: Electrostatics
The current implementation has analytical first derivative and thus allows energy minimizations, reaction path search (e.g., travel) and molecular dynamics simulations; SCC-DFTB/MM also works with Monte Carlo. Replica can also be used, which makes it possible to use replica path and related approaches (such the nudged elastic band) for determining reaction path with the SCC-DFTB/MM potential; along the same line, path integral simulations can be carried out as well, although only for equilibrium properties at this stage. Several aspects of the code will be improved in the near future, and new functionalities will be added:
1. Interface with centroid path-integral simulations and Tsallis statistics. 2. More flexible interface with BLOCK for general free energy simulations. 3. Better methods for open-shell systems; constrained density functional theories. 4. Time-dependent treatment for electronically excited states; non-adiabtic MD. 5. Integration with polarizable force field models (Drude).
File: SCCDFTB Node: GLNK, Up: Top, Next: Top, Previous: Status
Description of the GLNK Command
[GLNK atom-selection] atom-selection: contains a list of atoms that are boundary atoms.
Restrictions: see the correponding entry for GLNK in quantum.doc
Description: see the correponding entry for GLNK in quantum.doc
Limitations: The present implementation allows up to 5 QM-boundary atoms. To improve the geometry for the QM/MM boundary bond, an empirical correction (Ecor) term is added. Currently, Ecor parameters are only available for cases where the QM/MM partition cuts a C-C, a C-O, or a C-S bond. For other cases, no empirical corrections will be included. Unrestricted GHO-SCC-DFTB for open-shell system is not implemented.
Reference: Reference made to the following paper, which contains a more thorough description and discussion of test cases, is appreciated.
Jingzhi Pu, Jiali Gao, and Donald G. Truhlar, J. Phys. Chem. A 108, 5454-5463 (1998). "Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method." CHARMM Element doc/mndo97.doc $Revision: 1.2 $ # File: Mndo97, Node: Top, Up: (chmdoc/commands.doc), Next: Description
Combined Quantum Mechanical and Molecular Mechanics Method Based on MNDO97 in CHARMM
by Paul Bash ([email protected])
Additional modifications Kwangho Nam([email protected]) and Darrin York
* Menu:
* Description:: Description of the MNDO97 commands * Usage:: How to run MNDO97 in CHARMM * NEWD:: NEWD Command * Installation:: How to install MNDO97 in CHARMM environment
# File: mndo97, Node: Description, Up: Top, Next: Usage, Previous: Top
The MNDO97 QM potential is initialized with the MNDO97 command.
[SYNTAX CADPac]
MNDO97 [REMOve] [EXGRoup] (atom selection) [UNIT int] [GLNK atom-selection]
[NEWD int] ewald-spec
ewald-spec::= { [ KMAX integer ] } KSQMAX integer { KMXX integer KMXY integer KMXZ integer }
REMOve: Classical energies within QM atoms are removed.
EXGRoup: QM/MM Electrostatics for link host groups removed.
UNIT: Fortran unit for MNDO97 input file. (refere following example)
GLNK: GHO method implementation (refer qmmm.doc).
The syntax of the MNDO97 command in CHARMM follows closely that of the GAMESS command.
# File: Mndo97, Node: Usage, Up: Top, Next: NEWD, Previous: Description
For complete information about MNDO97 input see MNDO97 documentation.
A QM-MM job using MNDO97 needs two input files. The first is the normal CHARMM input file containing the MNDO97 command. The second file is the normal MNDO97 input file.
Mndo97 Input File ------For the MNDO97 input file all the keywords are required as for a stand alone MNDO97 calculation. The CHARMM minimizer is used so an MNDO97 run with only an energy and gradient calculation is necessary.
Examples ------An example of a MNDO97 input file to run with CHARMM: (for example, this file named as "mndo.inp")
iop=0 jop=-2 iform=2 igeom=1 + kharge=0 nprint=-5 mprint=-5 mminp=2 numatm=7 mmcoup=2 mmpot=7 mmfile=-1 ipsana=1 LYSINE
86 84.122 1 39.595 1 47.383 1 6 84.879 1 40.615 1 46.561 1 1 84.209 1 41.474 1 46.345 1 1 85.187 1 40.149 1 45.601 1 6 86.125 1 41.126 1 47.288 1 1 86.886 1 40.317 1 47.281 1 1 85.845 1 41.349 1 48.339 1 6 86.761 1 42.385 1 46.686 1 1 86.016 1 43.208 1 46.649 1 1 87.116 1 42.176 1 45.654 1 6 87.922 1 42.778 1 47.563 1 1 88.790 1 42.117 1 47.353 1 1 87.628 1 42.695 1 48.631 1 7 88.359 1 44.196 1 47.319 1 1 87.569 1 44.842 1 47.519 1 1 88.652 1 44.303 1 46.327 1 0 0.0000000000 0 0.0000000000 0 0.0000000000 0
See the documentation for MNDO97 for a description of the MNDO97 keywords. Each atom to be treated QM MUST be listed explicity in this MNDO97 input file. They MUST be in the same order as the CHARMM coordinate file. MNDO97 is called the first time using this input file and coordinates, and does an initial setup and calculates one energy and gradient. Subsequent energy and force calculations use coordinates from CHARMM data structures. Atom "86" above is a special "link" termination atom, which may be used instead of a hydrogen. This may work better in some instances than a hydrogen. Atom 86 is only parameterized for C-C single bond.
Current implementation has a limit is choosing non-bonded options. All atom based cutoffs methods is not fully supported for a certain boundary conditions such as periodic boundary condition. In any case, the QM-MM non-bond generation routine will only generate the non-bond list based on group-group separation scheme. Especially to use any periodic boundary conditions, it is strongly recomented to use group based cutoff scheme.
A sample shell script to run CHARMM with CADPAC is:
* Y160F simulation with NHDP isocitrate *
! open topology and parameter files open unit 10 form read name top_all22_prot_na.inp read rtf card unit 10 close unit 10 open unit 11 form read name par_all22_prot_na.inp read param card unit 11 close unit 11 bomb -3
! open appropriate coordinate file open unit 12 form read name lysn.pdb read sequ coor resi pdb unit 12 rewind unit 12 generate 7tim first none last none setup warn read coor resi pdb unit 12 close unit 12 update
! Before call MNDO command, MNDO97 input file should be opened ! and the unit of that file should be specified in MNDO command. ! ! call the MNDO command ! initial setup energy and gradient calculation ! It is possible at this point to run MNDO97 stand alone ! by changing the MNDO97 input to do a geometry optimization ! One would want to place a "stop" command after this command. open read unit 66 form name mndo.inp mndo unit 66 sele all end remo
! calculate the energy using coordinates from CHARMM energy
! do an energy minimization mini abnr nstep 500 nprint 1
! write out coordinates open unit 22 form write name lysn_min.pdb write coor pdb unit 22 * water * close unit 22 stop
To run MNDO97/CHARMM one may use the following script:
At the moment, MNDO97's input file needs to be opened before call MNDO. # File: Mndo97, Node: NEWD, Up: Top, Next: Installation, Previous: Usage
Description of the NEWE Command
[ NEWD int ] ewald-spec
ewald-spec::= { [ KMAX integer ] } KSQMAX integer { KMXX integer KMXY integer KMXZ integer }
A simple Ewald sum method is implemented into the QM/MM potential. A full description of theory is described in J. Chem. Theory. Comput. (2005) 1, 2. This is based on regular Ewald sum method and share similar keywords (see ewald.doc).
The defaults for the QM/MM-Ewald calculations are set internallya and are currently set to NEWD -1, KMAX=5, KSQMax=27, where the KMAX keyword is the number of kvectors (or images of the primary unit cell) that will be summed in any direction. It is the radius of the Ewald summation. For orthorombic cells, the value of kmax may be independently specified in the x, y, and z directions with the keywords KMXX, KMXY, and KMXZ. But, different from regular Ewald in CHARMM, it has no limitation on the shape of box, and can be used with PMEwald in MM part.
The KSQMax key word should be chosen between KMAX squared and 3 times KMAX squared, and KAPPA value share the exact same number you use in Nonbond options.
File: Mndo97, Node: Installation, Up: Top, Next: Top, Previous: NEWD
MNDO97/CHARMM interface status (February 1997)
- MNDO97, CADPAC, GAMESS and QUANTUM keywords cannot coexist in pref.dat
- The program runs on GNU, SGI, ALTIX, and IBMSP machines.
To compile MNDO97 with CHARMM one uses: install.com [machine] [size] W
The "W" specifies to compile and link MNDO97 with CHARMM. The MNDO97 code MUST be in a subdirectory called "mndo97q" that resides in $chmroot/source/mndint. mndint.src contains the QM/MM interface code. It is similar to cadint.src and gamint.src.
In $chmroot/source/mndint/mndo97q are files such as irixx.mak, aix4.mak, and etc. These files must be linked to machine.mak in order for the mndo97 code to compile properly for a given machine. For example, on the IBMSP aix4.mak was used to compile the code. install.com is already set up to make this link for both an IBMSP, GNU, ALTIX, and SGI. See install.com for details and to make changes for other machines. Also, located in $chmroot/source/mndint/mndo97q is a file called "changes_qmmm". This file lists changes made to the original mndo97 code required due primarily to conflicts with variable names in CHARMM. These variables may be changes in subsequent versions of MNDO97. CHARMM Element doc/cadpac.doc $Revision: 1.2 $
File: Cadpac, Node: Top, Up: (chmdoc/commands.doc), Next: Description
Combined Quantum Mechanical and Molecular Mechanics Method Based on CADPAC in CHARMM
by Paul Lyne [email protected]
* Menu:
* Description:: Description of the CADPAC commands * Using:: How to run CADPAC in CHARMM * Installation:: How to install CADPAC in CHARMM environment * Status:: Status of the interface code
File: Cadpac, Node: Description, Up: Top, Next: Usage, Previous: Top
The CADPAC QM potential is initialized with the CADPac command.
[SYNTAX CADPac]
CADPac [REMOve] [EXGRoup] (atom selection)
REMOve: Classical energies within QM atoms are removed.
EXGRoup: QM/MM Electrostatics for link host groups removed.
The syntax of the CADPAC command in CHARMM follows closely that of the GAMESS command.
File: Cadpac, Node: Usage, Up: Top, Next: Status, Previous: Description
For complete information about CADPAC input see Chapter 1 in the CADPAC distribution.
A QM-MM job using CADPAC needs four input files. The first is the normal CHARMM input file containing the CADPac command. The second file is the CADPAC input file specifying the basis set to be used and the Hamiltonian that is needed. The third and fourth files are libfil.dat and modpot.datrespectively. These are the library and model potential files that are supplied with CADPAC. Cadpac Input File ------For the CADPAC input file the following cards must be present: TITLE, BASIS, ATOMS, RUNTYP, START, FINISH.
TITLE: The keyword is always at the start of the input file and is followed by a one-line title on the next line of the input.
BASIS: This descirbes the basis set to be used for the QM region if a generic basis set is required. Examples include STO3G,321G,631G,321G*,631G*. These are the most common. Other basis sets are descibed in the CADPAC documentation. It is also possible to run a calculation using specific basis sets for individual atoms. If this feature is required then the BASIS keyword should be ommitted and the LIBRARY keyword is used for each atom in the QM region. For a more detailed description of the library command please refer to the official CADAPC documentation. All the basis sets that are supported by CADPAC are found in the files libfil.dat and modpot.dat.
ATOMS: This keyword is always required.
RUNTYP: For the purposes of QM-MM calculations this will either be ENERGY for a single point calculation or GRADIENT if the forces are also required. For any minimization or dynamics calculations the GRADIENT keyword should be used.
START: This keyword is always required.
FINISH: This keyword is always required.
Hamiltonians ------The Hamiltonian is HF unless otherwise specified. The Hamiltonian can be changed by inseerting the appropriate keyword after the RUNTYP key.
For example
MP2 Performs an MP2 calculation MP3 Performs an MP3 calcualtion CI Performs a Configuration Interaction calculatio (please refer to the official CADAPC manual)
For DFT calculations use the KOHNSHAM keyword: KOHNSHAM LDA MEDIUM GRDWT Performs an LDA calculation with a medium sized grid for numerical quadrature.
KOHNSHAM BLYP LARGE GRDWT Performs a non-local BLYP calculation with a large sized grid
For other functionals see the official CADPAC manual.
CADPAC I/O ------CADPAC has hard wired units 1,2 and 3 for the libfil.dat, modpot.dat and cadpac input file so avoid using these elsewhere in the CHARMM stream. Other units that CADPAC commonly uses for the grid, integrals etc are 13,14,18,35,53,and 54.
Examples ------An example of a CADPAC input file to run with CHARMM:
TITLE ! Required this is a test ! Put whatever you like on one line BASIS STO3G ! Generic basis set to be used ATOMS ! Required GRADIENT ! Run type. Use this for optimizations START ! Required FINISH ! Required
The above input file tells CADPAC to use an STO-3G basis for the atoms in the QM region. CADPAC will perform a gradient evaluation each time that it is called by CHARMM. If you require just a single point calculation without gradients just use ENERGY instead of GRADIENT. The input file above will perform a HF calculation. A DFT calculation is invoked as follows:
TITLE ! Required this is a test ! Put whatever you like on one line BASIS STO3G ! Generic basis set to be used ATOMS ! Required GRADIENT ! Run type. Use this for optimizations KOHNSHAM LDA MEDIUM GRDWT START ! Required FINISH ! Required
DF jobs are invoked by the KOHNSHAM card which takes the type of functional and grid to be used as arguments. In this case an LDA functional is used. Alternatives include BLYP, B3LYP. For details see the CADPAC distribution. A sample shell script to run CHARMM with CADPAC is:
#!/bin/tcsh -f # parameters: # 1 data file name # echo starting date echo $1 set HOME= {where CADPAC data files are} # data set and output in home directory # set data=$HOME/$1.inp set output=$HOME/$1.out2 # make a temporary directory to hold the workfiles cd /tmp mkdir $1 cd $1 # basis set library file assigned to fort.1 # pseudopotential library on fort.2 # the CADPAC input file is copied to UNIT 3 cp $HOME/$1.str fort.3 cp $HOME/$1.par . cp $HOME/libfil.dat fort.1 #cp $HOME/modpot.dat fort.2 # # run the program charmm.exe < $data rm -r ../$1
An example file can be found in test/c25test/cwat.inp. This input file also uses cwat.str and the sample run script runcwat.
File: Cadpac, Node: Status, Up: Top, Next: Top, Previous: Usage
CADPAC/CHARMM interface status (February 1997)
- CADPAC, GAMESS and QUANTUM keywords cannot coexist in pref.dat
- CADPAC recognizes atoms by their masses as specified in the RTF file
- The program runs on ALPHA, SGI, C90, IBMRS, HPUX platforms.
- There are references to a parallel version in the code. This has not been fully tested yet and so won't be included until a future release. CHARMM Element doc/diesel.doc $Revision: 1.1 $ # File: Diesel, Node: Top, Up: (chmdoc/commands.doc), Next: Description
Combined Quantum Mechanical and Molecular Mechanics Method Based on DIESEL(GAMESS) in CHARMM
by Milan Hodoscek ([email protected],[email protected])
Multi reference CI program DIESEL is connected to CHARMM program in a QM/MM method. To obtain the integrals for input to DIESEL program it is run from the GAMEss command.
* Menu:
* Description:: Description of the gamess commands. * Using:: How to run GAMESS in CHARMM. * Installation:: How to install GAMESS in CHARMM environment. * Status:: Status of the interface code. * Functionality:: Functionality of the interface code. # File: Diesel, Node: Description, Up: Top, Next: Usage, Previous: Top
The DIESEL QM potential is initialized with the GAMEss command.
[SYNTAX GAMEss]
GAMEss DIESel
In order to run DIESEL the standard GAMEss command must be used with the added DIESel keyword. The integer numbers after this keyword represent which energy is used in the CHARMM code for further processing.
DIESEL is the program to perform multi reference CI calculations.
# File: Diesel, Node: Usage, Up: Top, Next: Installation, Previous: Description
In order to run DIESEL with CHARMM one has provide separate input files for GAMESS (see gamess.doc) and for DIESEL. The information provided by GAMESS for DIESEL is the file which contains MO one and two electron integrals. In order to obtain such integrals one must specify RUNTYPE=MCSF in GAMESS control input. The follwing is an example for water with 3-21g basis set:
$CONTRL COORD=UNIQUE NOSYM=1 ICHARG=0 SCFTYP=mcscf $END $SYSTEM MEMORY=1400000 TIMLIM=100000 $END $BASIS GBASIS=N21 NGAUSS=3 $END $DET NCORE=1 NACT=6 NELS=8 $END $MCSCF maxit=1 micit=1 $end $DATA
$END This produces the necessary moints file which can be read by DIESEL input. This should be improved because we really don't need to run MCSCF, especially because it is very memory demanding. But it is currently the cheapest way to produce integrals over MO basis, without extensive modification of GAMESS. ???
Typical DIESEL script would be for example:
#! /bin/sh export DIESEL_EXE_DIR=/software/qc/diesel/1.14pre/Binaries/Intel cat <diesel.in MOIntegralFileFormat = GAMESSC1 MOLCASRootDir = `pwd` TempDir = `pwd`
NumberOfElectrons = 8 Multiplicities = { 1 } IrReps = { 0 } Roots = { 1 2 3 4 }
SelectionThresholds = { 1 1e-3 1e-5 } MaxDavidsonIters = 40 MaxHamiltonStorageMem = 100MB
!
$DIESEL_EXE_DIR/diesel
For complete information about DIESEL input see its own user's guide. In order to porvide the correct input files for GAMESS and DIESEL one has to spcify the following ENVIronment comands in CHARMM input script. envi input "h2o.str" envi output "h2o.gms" envi punch "test.dat" envi aoints "test.f8" envi moints "test.f9" envi dictnry "test.f10" envi work15 "test.f15" envi dasort "test.f20" envi dafl30 "test.f30" envi jkfile "test.f23" envi casints "test.f13" envi civectr "test.f12"
! For DIESEL envi dieselscript "CI.job" envi dieselout "dies.out"
DIESEL provides many energies (for various multiplicities and roots) in the same run. In order to get one of them for further processing (minimization for example; but be careful: no derivatives are available so one has to do very costly numerical calculation) the two integers after DIESEL keyword are for multiplicity and root, respectively. [NOTE: For complete example look at test/c28test/dieseltst.inp]
# File: Diesel, Node: Installation, Up: Top, Next: Status, Previous: Usage
Installation ------
To obtain the program write to Michael Hanrath ([email protected]). Since the program is written in C++ it was not practical to put it under CHARMM tree and compile them together. CHARMM only knows how to execute the script which runs DIESEL. DIESEL itsel is also just a driver for other programs. The only input it needs from GAMESS is the one and two electron binary file.
# File: Diesel, Node: Status, Up: Top, Next: Functionality, Previous: Installation
DIESEL/CHARMM interface status (February 2001)
- no derivatives in DIESEL
- C1 symetry
Problems to be solved:
- avoid running MCSCF
- cleanup the file name mess.
# File: Diesel, Node: Implementation, Up: Top, Next: Top, Previous: Functionality
Implementation ------
C++ is not very practical to compile with fortran programs so CHARMM/GAMESS and DIESEL are completely separated. When the integrals are transformed to MO basis by GAMESS, CHARMM calls system routine to run shell script for DIESEL. In it one has to specify the path to DIESEL distribution. CHARMM Element doc/charmmrate.doc # File: Polyrate, Node: Top, Up: (doc/charmmrate.doc), Next: Description
**************************************** * CHARMM/POLYRATE INTERFACE * ****************************************
CHARMMRATE: A Module for Calculating Enzymatic Reaction Rate Constants with POLYRATE and CHARMM
CHARMMRATE is an interface of CHARMM and POLYRATE to include quantum mechanical effects in enzyme kinetics. Although CHARMMRATE allows execution of POLYRATE with all existing capabilities, the present implementation is primarily intended for predicting reaction rates in enzyme-catalyzed reactions. CHARMMRATE can be combined with semiempirical combined QM/MM potentials with numerical second derivatives that are computed by the POLYRATE interface programs.
The rate constant for an enzymatic reaction depends on the transition state theory free energy of activation and on an overall transmission coefficient. Quantum effects on the degrees of freedom perpendicular to the reaction coordinate can be incorporated by means of a correction for quantum mechanical vibrational free energy, DeltaW_vib. As described by M. Garcia-Viloca, C. Alhambra, D. G. Truhlar, and J. Gao, in J. Chem. Phys. 114, 9953-9958 (2001), such a correction is calculated by carrying out projected instantaneous normal mode analysis at several configurations along a reaction coordinate as sampled by the umbrella sampling technique (or by any other suitable method) in molecular dynamics simulations with CHARMM. Note that projected instantaneous normal mode analysis involves projecting out the reaction coordinate of the potential of mean force (i.e., the coordinate along which umbrella sampling was carried out); thus it yields different frequencies and modes than would be obtained by ordinary instantaneous normal mode analysis. The correction for quantized vibrational free energy in modes normal to the PMF reaction coordinate is calculated from the average frequencies of the projected instantaneous normal mode analysis and is added to the classical potential of mean force.
The quantum effects on the reaction coordinate are represented by an averaged transmission coefficient obtained by carrying out variational transition state theory (VTST) calculations for individual members (configurations) of the transition state ensemble. These calculations involve a partition of the system into a frozen bath region and a dynamics region that is used in the dynamics calculation. CHARMMRATE has been used to determine the rate constants for the proton transfer reactions catalyzed by enolase and methylamine dehydrogenase and for the hydride transfer reactions catalyzed by alcohol dehydrogenase, xylose isomerase, and dihydrofolate reductase. These studies have demonstrated that inclusion of quantum effects is essential to calculate primary and secondary kinetic isotopic effects (KIEs) for hydrogen transfer reactions. The method used in these studies has evolved to its definitive form that includes free energy simulation to determine the free energy of activation and calculation of the transmission coefficient. Putting all the elements together yields a method that is called ensemble-averaged VTST with multidimensional tunneling (EA-VTST/MT),the formalism of which is presented in detail in the following recent papers:
C. Alhambra, J. C. Corchado, M. L. Sanchez, M. Garcia-Viloca J. Gao, and D. G. Truhlar J. Phys. Chem. B. 105, 11326-11340 (2001).
D. G. Truhlar, J. Gao, C. Alhambra, M. Garcia-Viloca, J. Corchado, M. L. Sanchez, and Jordi Villa, Acc. Chem. Res. 35, 341-349 (2002). M. Garcia-Viloca, C. Alhambra, D. G. Truhlar, and J. Gao, J. Comput. Chem. 2002, in press.
This documentation contains a short version and a long, detailed version following the short CHARMM-command description. Users are encouraged to read both parts.
* Menu:
* Description:: Description of the POLYRATE driver in CHARMM * Usage:: How to run POLYRATE in CHARMM * Installation:: How to install POLYRATE in CHARMM * Status:: Status of the interface code
# File: Polyrate, Node: Description, Up: Top, Next: Usage, Previous: Top
**************************************************** * Syntax for the CHARMMRATE Method * ****************************************************
POLYRATE is initiated with the POLYrate command.
[Syntax POLYrate]
POLYrate [ atom-selection] [RUNIT int] [PUNIT int] [TSUNit int] [OPUNit int] [PMFZpe ] [ATMA int ] [ATMB int] [ATMC int] [POLYRATE commands] .... [*finish] atom-spec::= {residue-number atom-name} {segid resid atom-name} {BYNUm atom-number}
RUNIt int: Unit specification for input of initial coordinates of the reactant species. The current limitation is that only CHARMM format is allowed for the coordinate file.
PUNIt int: Unit specification for input of initial coordinates of the product species. The current limitation is that only CHARMM format is allowed for the coordinate file.
TSUNit int: Unit specification for input of initial coordinates of the transition state. The current limitation is that only CHARMM format is allowed for the coordinate file.
OPUNit int: Unit to write out coordinates of the optimized structures, of any of the reactant, product, and TS, depending on the species being optimized. The current limitation is that only CHARMM format is used.
PMFZpe ATMA int ATMB int ATMC int: this command switches on the projection operator that is used to project the reaction coordinate out of the Hessian matrix of the system. This is used for projected instantaneous normal mode analysis. The reaction coordinate is defined as the difference in bond distance between the breaking and making bonds. ATMA int: atom number for the donor atom following the numbering in the general section of POLYRATE commands (see below).
ATMB int: atom number for the transferring atom following the numbering in the general section of POLYRATE commands (see below).
ATMC int: atom number for the acceptor atom following the numbering in the general section of POLYRATE commands (see below).
[POLYRATE commands]
This section contains standard POLYRATE commands. They must follow immediately after the [POLYrate] command in the CHARMM input stream. This section is terminated by the key word [*finish], lower case with a star in the beginning. For details of the POLYRATE commands, see the POLYRATE documentation.
# File: Polyrate, Node: Usage, Up: Top, Previous: Description, Next: Installation
Note: The version number of CHARMMRATE is 2.0/C28b3-P9.0. This means that CHARMMRATE-version 2.0 is based on POLYRATE-version 9.0 and CHARMM-version c28b3. The version number may be abbreviated to 2.0 when no confusion will result.
CHARMMRATE is a module of CHARMM for interfacing it with POLYRATE; the POLYRATE main program becomes a subprogram of CHARMM. POLYRATE can be called to carry out projected instantaneous normal mode analysis and variational transition state theory calculations with semiclassical multidimensional tunneling contributions. When POLYRATE needs the value or gradient of the potential energy surface, it calls a set of interface routines called hooks. The hooks in turn call CHARMM routines for energies and gradients calculated by molecular mechanics or QM/MM methods. The current version has not been parallelized.
Referencing for CHARMMRATE:
"The rate constant (or reaction path or geometry optimization, etc.) calculations were carried out using the CHARMMRATE program[1-3]".
[1] M. Garcia-Viloca, C. Alhambra, J. C. Corchado, M. L. Sanchez, J. Villa, J. Gao, and D. G. Truhlar, CHARMMRATE-version 2.0, University of Minnesota, Minneapolis, 2002, a module of CHARMM (Ref. 2) for interfacing it with POLYRATE (Ref. 3).
[2] Chemistry at HARvard Macromolecular Mechanics (CHARMM) computer program, as described in B. R. Brooks, R. E. Bruccoleri, B. D. Olafson , D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
[3] J. C. Corchado, Y.-Y. Chuang, P. L. Fast, J. Villa, W.-P. Hu, Y.-P. Liu, G. C. Lynch, K. A. Nguyen, C. F. Jackels, V. S. Melissas, B.J. Lynch, I. Rossi, E. L. Coitino, A. Fernandez-Ramos, J. Pu, and T. V. Albu, R. Steckler, B. C. Garrett, A. D. Isaacson, and D. G. Truhlar, POLYRATE-version 9.0, University of Minnesota, Minneapolis, 2002. # File: Polyrate, Node: Installation, Up: Top, Next: Status, Previous: Usage
**************************************************** * Availability of CHARMMRATE * ****************************************************
CHARMMRATE-version 2.0/C28b3-P9.0 is a module of CHARMM-version c28b3 for interfacing it with POLYRATE-version 9.0. An earlier version, CHARMMRATE-version 1.0, was distributed as part of the CHARMM program beginning with version 28b1 of CHARMM and was used to interface previous versions of CHARMM and POLYRATE. CHARMMRATE-2.0/C28b3-P9.0 will be distributed beginning with version c28b3 of CHARMM. The user will also require the CRATE utility for modifying POLYRATE to make it compatible with CHARMM. CRATE-version 8.11 corresponds to CHARMMRATE-1.0, and CRATE-version 9.0 corresponds to CHARMMRATE-2.0. CRATE-version 9.0 corresponds to interfacing POLYRATE-version 9.0. The prospective user of CHARMMRATE should obtain a valid license for CHARMM from an authorized CHARMM licenser and valid licenses for POLYRATE and CRATE from the University of Minnesota (http://comp.chem.umn.edu).
# File: Polyrate, Node: Status, Up: Top, Next: Top, Previous: Installation
1. INTRODUCTION
CHARMMRATE is an interface of CHARMM and POLYRATE to include quantum mechanical effects in enzyme kinetics. Although CHARMMRATE allows execution of POLYRATE with all existing capabilities for reactions with only one reactant and only one product, the present implementation is primarily intended for prediction of the reaction rates of enzyme-catalyzed reactions. Any CHARMMRATE calculation involves the partition of the system into a primary subsystem (or primary-zone atoms), which contains the subset of atoms involved in the reaction, and the rest of the system (secondary-zone atoms). Only the coordinates of the primary-zone atoms are passed from CHARMM to POLYRATE for both projected instantaneous normal mode analysis and dynamics calculations. Consequently, the quantum mechanical vibrational correction and the dynamics effects are calculated for the primary subsystem in the field of the secondary subsystem.
1.A. Capabilities added to CHARMM by CHARMMRATE and references for methods
POLYRATE includes a very large number of options and has multiple capabilities. The user of CHARMMRATE is encouraged to read the POLYRATE manual to learn more about these capabilities. The present section summarizes a few of the capabilities that are liable to be of most interest to CHARMMRATE users.
1.A.1. Transition state optimization
Saddle point geometry optimizations for the primary (dynamic) zone in the frozen protein-plus-solvent bath may be performed in various ways; the default option is the Newton-Raphson method with Brent line minimization as described in W. H. Press, S. P. Flannery, S. A. Teukolsky, and W. T. Vetterling, Numerical Recipes (Cambridge University Press, Cambridge, 1986), p.254. The default option for optimization of the stationary points for reactants and products is to use the BFGS method that has been implemented in POLYRATE. See the POLYRATE manual for further information about the optimization methods available in POLYRATE.
1.A.2. Reaction path
In general, reaction paths (RPs) may be defined in various ways. The simplest general method that is reasonably sure to give physically meaningful vibrational frequencies for motions transverse to the reaction path (and hence also physically meaningful free energy of activation profiles) is the steepest descents path in isoinertial coordinates. (An isoinertial coordinates system is one in which the kinetic energy is a sum of square terms and the coordinates are scaled or weighted so that each kinetic energy term has the same reduced mass. All isoinertial coordinate systems are related to each other by orthogonal transformations, and steepest descents paths are invariant under orthogonal transformations.) A steepest descents path is also called a minimum energy path (MEP). The signed distance from the saddle point along the reaction path is called the reaction coordinate, usually denoted s. (This reaction coordinate, s, should not be confused with the reaction coordinate used for umbrella sampling, which is called z.) The isoinertial MEP is sometimes just called the MEP, or it may just be called the RP; other workers prefer to append the word intrinsic, e.g., intrinsic MEP, intrinsic reaction path, intrinsic reaction coordinate, etc.
In CHARMMRATE, the reaction path refers to a multidimensional path for the primary-zone (dynamic) atoms in the presence of the secondary- zone (frozen) atoms.
CHARMMRATE may be used to calculate the isoinertial minimum energy path (MEP) as described in B. C. Garrett, M. J. Redmon, R. Steckler, D. G. Truhlar, K. K. Baldridge, D. Bartol, M. W. Schmidt, M. S. Gordon, J. Phys. Chem. 92, 1476-1488 (1988).
1.A.3. Free energy of activation profile and variational transition state theory
Vibrational partition functions and generalized free energies of activation (which are free energies of activation for tentative transition states that are not necessarily associated with either a saddle point or with the final variational transition state) are computed along the reaction path by using the quantum mechanical harmonic oscillator approximation in 3N1 - 1 degrees of freedom, where N1 is the number of atoms in the primary zone, and the reaction coordinate is projected out. This kind of calculation is described in S. E. Wonchoba, and D. G. Truhlar, J. Chem. Phys. 99, 9637- 9651 (1993). The generalized free energy of activation as a function of the reaction coordinate (which is the signed distance along the MEP) is called the free energy of activation profile, and it may be used to calculate reaction rate constants by variational transition state theory (VTST) as described in D. G. Truhlar and B. C. Garrett, Acc. Chem. Res. 13 , 440-448 (1980). A procedure like this was used in C. Alhambra, J. Gao, J. C. Corchado, J. Villa, and D. G. Truhlar, J. Am. Chem. Soc. 121, 2253-2258 (1999), but it is now recommended to use the more complete EA-VTST/MT method, in which this quantity is used to compute a transmission coefficient rather than a rate constant. VTST for a canonical ensemble (i.e., a system at a fixed temperature) is also called canonical variation theory (CVT). In the EA-VTST/MT method (described in Section 2), this step is carried out for several members of the transition state ensemble, and it is used for the quasiclassical part of the ensemble-averaged transmission coefficient.
1.A.4. Transmission coefficient
In CHARMMRATE the EA-VTST/MT transmission coefficient has two parts: a quasiclassical dynamical recrossing part (Section 1.A.3) and a part that accounts for tunneling (transmission through the barrier at energies below the top) and non-classical reflection (reflection caused by diffraction from the barrier top even when the energy is above the barrier); often we just refer to the combination of tunneling and non-classical reflection effects as tunneling (the tunneling is more important than the non- classical reflection because the energies where tunneling occurs have larger Boltzmann factors than the energies where non-classical reflection occurs).
CHARMMRATE can calculate the tunneling part of the transmission coefficient in various ways. The most complete method is the microcanonical optimized multidimensional tunneling (muOMT) approximation as described in Y.-P. Liu, D.-h. Lu, A. Gonzalez-Lafont, D. G. Truhlar, and B. C. Garrett, J. Am. Chem. Soc. 115, 7806-7817 (1993). In this calculation, tunneling and non-classical reflection along the reaction path are included by calculating both the large-curvature tunneling (LCT) approximation and the small-curvature tunneling (SCT) approximation and, at each tunneling energy, accepting whichever tunneling approximation yields the larger tunneling probability. This is a poor man's version of a more complete search for the semiclassical tunneling paths that minimize the imaginary action integrals, and it has been extensively validated as summarized by T. C. Allison and D. G. Truhlar, in Modern Methods for Multidimensional Dynamics Computations in Chemistry, edited by D. L. Thompson (World Scientific, Singapore, 1998), pp. 618-712.
One may also limit the calculation to just the LCT or SCT approximation or to the zero-curvature tunneling approximation (ZCT) or even the Wigner approximation. The muOMT, LCT, SCT, and ZCT approximations are multidimensional, whereas the Wigner approximation is one-dimensional. The ZCT approximation calculates tunneling along the isoinertial MEP, whereas the muOMT, LCT, and SCT approximations include various amounts of corner cutting, i.e., tunneling on the concave side of the isoinertial MEP, with the amount and nature of the corner cutting depending on the curvature of the reaction path. The computational cost decreases in the following order: muOMT, LCT, SCT, ZCT, Wigner. When tunneling is included, the EA-VTST/MT rate constant is written as
k(T) = gamma(T) kTST(T) where kTST(T) is the TST rate constant that is determined by the free energy simulation of of stage 1 (including the quantum mechanical correction of step 2 of stage 1), and gamma(T) is the transmission coefficient that accounts for classical recrossing (the quasiclassical part of section 1.A.3) and for tunneling and non-classical reflection.
Background for the calculation of KIEs by VTST with multidimensional tunneling approximations is given in D.G. Truhlar, D.-h. Lu, S.C. Tucker , X.G. Zhao, A. Gonzalez-Lafont, T.N. Truong, D. Maurice, Y-.P. Liu, and G.C. Lynch, in Isotope Effects in Chemical Reactions and Photodissociation Processes, edited by J. A. Kaye (American Chemical Society Symposium Series 502, Washington, DC, 1992), pp. 16-36.
1.B. CHARMMRATE capabilities that are not included either in POLYRATE or in prior versions of CHARMM: Projected instantaneous normal mode analysis
Two source files of POLYRATE (see the CRATE manual) are modified by the CRATE utility version-9.0 to carry out projected instantaneous normal mode analysis. With these routines quantum mechanical harmonic frequencies of the vibrational modes of the primary subsystem orthogonal to the reaction coordinate may be calculated for a given configuration of the system. This calculation is used in the second step of the first stage of the EA-VTST/MT method (described in Section 2) to include quantum effects on the 3N-7 highest-frequency vibrational modes of the primary zone in a hypersurface orthogonal to the reaction coordinate that is used for umbrella sampling in the first step of stage 1. The constraint that the modes obtained are orthogonal to the reaction coordinate is achieved by a projection operator described in C. Alhambra , J. C. Corchado, M. L. Sanchez, M. Garcia-Viloca, J. Gao, and D. G. Truhlar J. Phys. Chem. B 105, 11326-11340 (2001).
1.C. CHARMM options that are of particular interest for use with CHARMMRATE.
CHARMMRATE is of particular interest for calculations of rate constants for enzymatic reactions. Although the program would allow the use of pure molecular mechanics (the CHARMM22 force field) for such calculations, combined quantum mechanical and molecular mechanical (QM/MM) potentials are much more realistic than pure molecular mechanics for chemical reactions. Using CHARMM, QM/MM calculations can now be performed at the ab initio level using GAMESS (B. Brooks and M. Hodoscek, unpublished results), at the density functional level using CADPAC (P. D. Lyne, M. Hodoscek, and M. Karplus, J. Phys. Chem. A 103, 3462-3471 (1999)), and at semiempirical molecular orbital levels (AM1 and PM3, with general parameters or with specific reaction parameters) with MOPAC (M. J. Field, P. A. Bash, and M. Karplus, J. Comput. Chem. 11 700-733 (1990)). There is more than one choice for joining the QM subsystem to the MM one. The first choice is to use "link atoms" to saturate the valence of the fragment; this requires that certain atomic charges in the MM fragment that are close to the QM region be deleted to avoid artificial polarization of the quantum subsystem. One possibility to avoid these problems is to use the generalized hybrid orbital (GHO) method described in J. Gao, P. Amara, C. Alhambra, and M. Field, J. Phys. Chem. A 102, 4714-4721 (1998). The GHO method is currently available for semiempirical calculations with the AM1 and PM3 methods, and it is being extended (work in progress) to ab initio and DFT methods. Another way to correct the link atom artifacts in the original formulation is proposed in C. Alhambra, L. Wu, Z.-Y. Zhang, and J. Gao, J. Am. Chem. Soc. 120, 3858-3866 (1998).
Molecular dynamics simulations of an enzyme-solvent system can be carried out on a QM/MM potential energy surface either using periodic boundary conditions or using stochastic boundary conditions; for the periodic boundary conditions see M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, (Oxford University Press, New York, 1987), Ch. 1, and for the stochastic boundary conditions see C. L. Brooks, A. Brunger, and M. Karplus, Biopolymers 24, 843-865 (1985). Free energy perturbation and umbrella sampling techniques can be used to determine the potential of mean force or classical free energy profile for the enzymatic reaction (see C. Alhambra, L. Wu, Z.-Y. Zhang, J. Gao, J. Am. Chem. Soc. 120, 3858-3866 (1998)). 2. THEORETICAL BACKGROUND: Ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT).
This section of the manual summarizes the theoretical framework and the practical procedure for the EA-VTST/MT method developed in C. Alhambra, J. C. Corchado, M. L. Sanchez, M. Garcia-Viloca, J. Gao, and D. G. Truhlar J. Phys. Chem. 105, 11326-11340 (2001).
The capabilities added to CHARMM by CHARMMRATE allow the user to calculate the rate constant for an enzymatic reaction with the EA-VTST/MT procedure.
The rate constant for an enzymatic reaction, which is a unimolecular process, is obtained by combining free energy simulations and variational transition state theory (VTST) with microcanonical optimized multidimensional tunneling contributions (muOMT), both in the presence of the protein environment. The potential energy surface (PES) is modeled by a QM/MM method, for example by a semiempirical MO method combined with the CHARMM force field and with the generalized hybrid orbital method (GHO) to treat the boundary between the QM and the MM parts of the system. In addition, a semiempirical term (see quantum.doc LEPS command) or specific reaction parameters (SRP) may be used to improve the accuracy of the PES.
The rate constant is expressed as a function of the free energy of activation, DeltaGCVTact, calculated by variational transition state theory free energy molecular dynamics simulations, and the transmission coefficient, gamma. There are two versions of the method that differ in the approximation used to evaluate gamma, in particular a 2-stage version and a three-stage version. The procedure for the former approximation, which has been applied in the study of five hydrogen transfer reactions, has the following two stages:
1) In stage 1 of the calculation, the free energy of activation, including the quantum mechanical vibrational free energy, is computed. This involves the following calculations:
Step 1 - Calculation of the classical mechanical (CM) or transition state theory free energy of activation by computing the potential of mean force (PMF) along a distinguished reaction coordinate. For a reaction
AB + C -> A + BC, the reaction coordinate, z, may be defined as:
z = rAB - rBC
The CM PMF can be evaluated by carrying out classical molecular dynamics on a QM/MM potential energy surface with the umbrella sampling technique implemented in CHARMM (see umbrel.doc) or free energy perturbation theory. Note, for the discussion below that umbrella sampling involves a sequence of overlapping windows (whose centers are separated by about 0.1-0.2 angstroms), each of which is later divided into 50-100 bins. The bins are typically 0.01 angstroms wide. (These specific numerical values are just given as examples; none of these quantities is restricted to lie within those limits.)
Step 2 - Calculation of the quantum mechanical vibrational free energy correction, DeltaW_vib, which is the difference between the quantal vibrational free energy and the classical vibrational free energy. The addition of DeltaW_vib to the CM PMF gives the quasi-classical (QC) PMF. DeltaW_vib may be evaluated by carrying out projected instantaneous normal mode analysis for the primary-zone atoms for many configurations (100-400 per window) obtained in the umbrella sampling step (see Section 1.B). The projected instantaneous normal mode frequencies obtained for the different configurations in a given bin may be averaged and the averaged value used to determine DeltaW_vib. Strictly speaking, one might argue that one should average the squared frequencies or some Boltzmann factors, but in initial applications it has been found sufficient to average the frequencies themselves.
After these two steps, the value of z with highest QC free energy is called z*, and the bin containing z* (or a small set of bins centered on this bin) defines the ensemble of configurations that are representative of the transition state of the enzymatic reaction.
2) Stage 2 has the objective of computing the transmission coefficient, gamma (T), that is the average over transition state configurations i of the product of two factors, Gamma_i and kappa_i. The first factor, Gamma_i, which is the the quasiclassical transmission factor, corrects the rate constant for classical mechanical dynamical recrossing. The second factor, kappa_i, is the semiclassical transmission coefficient that accounts mainly for tunneling, that is, the quantum mechanical effect on the reaction coordinate, which is missing in the calculation of the QC rate constant. The averaged transmission coefficient is:
gamma =
The approximation described here to obtain the transmission coefficients is called static secondary-zone approximation (SSZ). The product of the averaged transmission coefficient obtained in this way and the quasiclassical rate constant of stage 1 results in the SSZ version of the EA-VTST/MT rate constant. The results obtained in five studies of enzymatic hydrogen transfer reactions demonstrate that the SSZ rate constant is accurate enough to reproduce experimental KIEs.
The SSZ result may be improved by carrying out a further step that has been called stage 3. In stage 3, the free energy of the secondary zone is calculated by free energy perturbation theory along the minimum- energy paths of stage 2. This allows us to include the secondary-zone free energy in the transmission coefficient. This is called the equilibrium-secondary-zone (ESZ) approximation.
The EA-VTST/MT method is described in: C. Alhambra, J. C. Corchado, M. L. Sanchez, M. Garcia-Viloca, J. Gao, and D. G. Truhlar J. Phys. Chem. B 105, 11326-11340 (2001), and in D. G. Truhlar, J. Gao, C. Alhambra, M. Garcia-Viloca, J. Corchado, M. L. Sanchez, and J. Villa, Acc. Chem. Res. 35, 341-349 (2002). A complete description of an application study is provided in M. Garcia-Viloca, C. Alhambra, D. G. Truhlar, and J. Gao, J. Comput. Chem. 2002, in press.
3. PROGRAM STRUCTURE
3.A. Overall design
The CHARMMRATE interface for CHARMM and POLYRATE takes advantage of the modular nature of both programs, and, consequently, minimal modifications of CHARMM and POLYRATE were required. The CHARMM program is the main driver of the integrated program, which makes a FORTRAN call to the interface subprogram, CHARMMRATE, to initiate calculations by POLYRATE. The energy and energy gradients for the primary-zone atoms required by POLYRATE are determined by CHARMM through the interface subprogram and are supplied to POLYRATE through a set of subroutines called the POLYRATE hooks.
3.B. Modifications and additions to CHARMM
Only two modifications have been made in the CHARMM program: (1) addition of a one-line keyword processing command in the charmm_main.src module to initiate the subroutine call to CHARMMRATE; (2) addition of the CHARMMRATE module.
3.C. Modifications and additions to POLYRATE
Specific modifications of the original POLYRATE program have been made primarily for efficient transfer of information between CHARMM and POLYRATE and to eliminate conflicts and other problems during compilation. These modifications are described in the CRATE manual, available at http://comp.chem.umn.edu/crate.
4. INSTALLATION OF charmmrate AND ITS USE
4.A. Program distribution
CHARMMRATE-version 2.0/C28b2-P9.0 is distributed as a module in CHARMM. CHARMM is a copyrighted program distributed by Professor Martin Karplus's research group at Harvard University and by Accelrys, Inc. In addition to CHARMM,which includes the CHARMMRATE module, users also need to obtain the POLYRATE program, which is a copyrighted program distributed by the University of Minnesota (http://comp.chem.umn.edu) and the CRATE utility, also available from Minnesota. The CRATE utility will make the changes to the source code of POLYRATE to allow the interface between the two programs. When the CHARMM program (which, beginning with version 28, automatically includes the CHARMMRATE module), the POLYRATE program and the CRATE utility have been obtained, integration of the codes into a single executable file is straightforward as described below.
4.B. Installation The user should carry out the following steps:
1. Install CHARMM.
2. Store the tar file polyrate9.0.tar.Z (obtained from the University of Minnesota, http://comp.chem.umn.edu) in the directory chmroot/source/prate and untar it with this command:
tar xvf polyrate9.0.tar
3. Set an environmental variable, called pr, to the absolute path name of the directory where the polyrate program is stored. Example:
C shell % setenv pr /home/chmroot/source/prate/polyrate9.0 Bourne shell $ pr = /home/chmroot/source/prate/polyrate9.0 $ export pr
4. Store the tar file crate9.0.tar.Z (obtained from the University of Minnesota, http://comp.chem.umn.edu) in the directory chmroot/source/prate and untar it with this command:
tar xvf crate9.0.tar
The directory crate9.0 will then contain the files required to prepare POLYRATE for use with the CHARMMRATE module of CHARMM. These files are described in the CRATE manual. Change the dimensions specified in the param.inc file located in the newly created directory, crate9.0, in order to make them large enough for the system(s) to be studied, but small enough to run in the memory available on the computer chosen to carry out the work. Or use the param.inc file distributed as part of CRATE. See the POLYRATE manual for further discussion of the dimensions in in POLYRATE.
5. Set an environmental variable, crate, to the absolute path name of the directory where the CRATE package is stored.
Example:
C shell % setenv crate /home/chmroot/source/prate/crate9.0 Bourne shell $ crate = /home/chmroot/source/prate/crate9.0 $ export crate
6. Go to the /build directory of CHARMM, i.e. cd /home/chmroot/build/'chm_host', and edit the file pref.dat. Add the CHARMMRATE module to the list.
7. If CHARMM has been compiled previously without POLYRATE, remove all the object files in home/chmroot/lib/'chm_host'
8. Go to the CHARMM directory chmroot and type the command: install.com 'chm_host' (small/medium/large) POLYR > & log & (see install.doc in the CHARMM documentation directory). This step will execute the script install_cr.com, which will put the CHARMMRATE source code in the directory /home/chmroot/source/prate. Any modifications desired should be done here.
9. You do not need to run the script install_cr.com (described in the CRATE manual) in any further compilations. Therefore it is recommended to comment the following line in the file /home/chmroot/install.com: $crate/install_cr.com
10. After compilation, you will have a new executable in: /home/chmroot/exec/'chm_host'
NOTE: In order to run projected instantaneous normal mode analysis with CHARMMRATE-version 2.0 it is necessary to do small changes in two of the files located in the directory /home/chmroot/source/prate after the compilation process described above. Instructions for these changes are provided in the README file contained in the crate9.0 directory of the CRATE package.
5. DESCRIPTION OF INPUT
CHARMMRATE is run from the CHARMM main input stream. The syntax to execute polyrate from charmm's input stream for a reaction with only one reactant (e.g., an enzyme-substrate precursor complex) and only one product (e.g., an enzyme-substrate successor complex) is:
POLYrate SELEction { atom-spec } end [RUNIt int] [PUNIt int] [TSUNit int] [OPUNit int] [ PMFZpe ] [ATMA int ] [ATMB int] [ATMC int] _polyrate_input_ *finish
We note the use of the CHARMM convention by which one needs to enter only the first four letters of POLYrate and other words with the first four letters capitalized. Furthermore the parts in brackets are optional. The meanings of the various keywords are:
SELEction { atom-spec } specifies the primary-zone atoms in POLYRATE:
atom-spec = { residue-number atom-name } { segid resid atom-name } { BYNUm atom-number }
RUNit int: Unit specification for input of initial coordinates of the reactant species. The current limitation is that only CHARMM format is allowed for the coordinate file.
PUNit int: Unit specification for input of initial coordinates of the product species. The current limitation is that only CHARMM format is allowed for the coordinate file.
TSUNit int: Unit specification for input of initial coordinates of the transition state. The current limitation is that only CHARMM format is allowed for the coordinate file.
OPUNit int: Unit to write out coordinates of the optimized structures of the reactant, product, or TS, depending upon which of these is requested (elsewhere) to be written. The current limitation is that only CHARMM format is used. The coordinate files assigned to these units must be in the CARD format (see CHARMM documentation for details).
PMFZpe ATMA int ATMB int ATMC int: this command switch on the projection of the reaction coordinate out of the Hessian matrix of the system. It is used for projected instantaneous normal mode analysis. The reaction coordinate is defined as the difference in bond distance between the breaking and making bonds.
ATMA int: atom number for the donor atom following the numbering in the general section of POLYRATE commands (see below).
ATMB int: atom number for the transferring atom following the numbering in the general section of POLYRATE commands (see below).
ATMC int: atom number for the acceptor atom following the numbering in the general section of POLYRATE commands (see below).
_polyrate_input_: This section contains a standard POLYRATE fu5 input file. It must follow immediately after the POLYrate command in the CHARMM input stream. For details of POLYRATE input, see the POLYRATE documentation. The initial coordinates have already been setup through the POLYrate command; therefore the GEOM record in the POLYRATE fu5 input file may be omitted. If, however, the GEOM record is present, the Cartesian coordinates given in this record will replace the data set up through the POLYrate command. This is not recommended.
*finish The last record to be read by POLYRATE from the CHARMM main input stream. This will terminate I/O operations from unit 5 by POLYRATE, and POLYRATE calculations will proceed.
6. TEST RUNS
This section describes two test runs. Each test job includes a full input file, initial coordinates and parameter files. They are located in:
/home/chmroot/test/cquantumtest.
6.1. Test Job 1 - Direct dynamics of chorismate to prephenate in the gas phase
This test job reads in three initial guess coordinates for the reactant state, product state, and transition state, optimizes their geometries, and performs a CVT calculation to yield the predicted rate constants at various temperatures. This test job takes roughly 3 hours on an SGI Octane 2 computer running under the Irix 6.5 operating system. (Test Job 2 is a shorter test run.)
6.1.A. Input files
The cr01.inp file contains the CHARMM input stream for a direct dynamics calculation of the chorismate to prephenate rearrangement reaction. Similar calculations can be carried out for the substrate in the enzyme active site, provided that appropriate boundary conditions are set up in he CHARMM input. The charmm22.top and charmm22.par files are the CHARMM topology and parameter files. They are required for all CHARMM calculations.
Three coordinate files are provided for this test job, corresponding to the initial guess coordinates for the reactant (gs.crd), product (prod.crd), and transition state (ts.crd) for the dynamics calculation with POLYRATE.
6.1.B. Description of the CHARMM input stream
The majority of the CHARMM commands are straightforward. The three initial guess coordinate files must be opened as formatted files in the CHARMM input stream before the POLYrate command is initiated. Certain FORTRAN unit numbers are default file choices in POLYRATE. Therefore, these numbers should not be used in the CHARMM input file unless the POLYRATE defaults are changed. Please consult the POLYRATE documentation for a full list and description of these files.
Five (5) FORTRAN files will be used by POLYRATE to write out the computational results. They are files with unit numbers 14, 25, 26, 27, and 61, which should be opened in the CHARMM input stream before CHARMMRATE calculations.
Section 6.1.C summarizes the contents of these files.
All input instructions immediately following the POLYrate command are those of POLYRATE. A full description of these commands can be found in the POLYRATE documentation.
6.1.C. Description of CHARMMRATE output
cr0114.out - computed reaction rates at various temperatures using the TST and CVT methods.
cr0125.out - potential energy along the reaction coordinate s, which measures distance along the minimum energy path (MEP), and computed transmission coefficient, if requested. Since the test run is for a CVT calculation, no multidimensional tunneling is included in the test run.
cr0126.out - computed vibrational frequencies that hgave been requested for printing out along s.
cr0127.out - coordinates along s.
cr0161.out - optimized geometries, energies, vibrational frequencies and the Hessian for the reactant, product, and transition state.
6.2. Test Job 2 - Geometry optimization of chorismate in a water bath
This test job performs geometry optimization of chorismate in the presence of a frozen water bath, arbitrarily taken from the trajectory of a molecular dynamics simulation of chorismate in water.
The cr02.inp file is the CHARMM input stream command file. In addition to the CHARMM topology and parameter files, the cr02.crd file is required; it contains the instantaneous (initial) coordinates of chorismate in water from a molecular dynamics simulation.
The file optcr02.crd contains the optimized coordinates of chorismate in water. CHARMM Element doc/cheq.doc $Revision: 1.4 $ # File: CHEQ, Node: Top, Up: (chmdoc/commands.doc), Next: Description
The CHarge EQuilibration Method
The CHEQ and associated modules implement polarization via the fluctuating charge method as based on the CHarge EQuilibration methods outlined in the literature. While the current forcefield parameters are valid for most small molecules and proteins, the force field is constantly undergoing refinement and development.
The electrostatic model derives formally from the density functional theory of atoms in molecules; polarization is effected as a result of chemical potential equalization everywhere within a molecule, forcing charge flow from regions of high to low chemical potential based on atomic properties. These properties are the atomic hardness and electronegativity. The parameters are treated as such and are determined from fits to density functional calculations of charge responses and mono- and dipole moments of small molecules in vacuum.
The method can be used to perform energy, minimization, and dynamics calculations for the above-mentioned systems. For dynamics, the charges are coupled to Nose- Hoover baths to maintain proper adiabaticity. Several normalization schemes are allowed to maintain charge constant over desired partitions. Several water models are supported including the SPC-FQ and TIP4P-FQ models of Rick et al.
* Menu:
* Description:: Description of the CHEQ Function * Syntax:: Syntax of the CHEQ commands * Options:: CHEQ Command Options * Energy:: Usage with Energy and Dynamics commands * Scalar:: Usage with the Scalar Command * Examples:: Usage Example Script * Mixed Systems:: Mixed Polarizable / Non-Polarizable Systems (FQ/MM) * References:: References for CHEQ Methods
# File: CHEQ, Node: Description, Up: Top, Previous: Top, Next:Syntax
The CHarge EQuilibration routines implement the fluctuating charge dynamics as described in recent literature (1-9). The method derives from the density functional theory of atoms in molecules. The model is a relatively simple approach to incorporate a means for electronic density rearrangement (as reflected grossly in terms of some partitioned 'charge' on an atom) due to changes in chemical environment---polarizability. The mechanism for the redistribution is the equalization of electronic chemical potential everywhere within a molecule, a statement of Sanderson's principle of electronegativity equalization ( since, in DFT, the chemical potential and electronegativity are analogous). The electrostatic potential adopted in this formalism is (for a system with M molecules with N_i atoms in molecule 'i': __ __ / \ N N_i M M | N N | E = sum sum CHI_ia(0) Q_ia + 1/2 sum sum | sum sum ETA_iajb Q_ia Q_jb | i=1 a=1 i=1 j=1 | a=1 b=1 | \__ __/
The ETA_iajb term comes from the hardness matrix whose elements are determined via (Ref. 13):
1/2 ( ETA_i + ETA_j) ETA_ij = ------sqrt( 1 + 0.25 (ETA_i + ETA_j)**2 R_ij**2)
Atoms involved in bonded interactions, angle interactions, and dihedral interactions interact with each other via the combination rule. Atoms in a molecule separated by more than three bonds interact with the normal Coulomb 1/R interaction, as do charge sites on different molecules.
The model requires parameterization of atomic electronegativities and hardnesses. The hardness are determined via fitting the DFT charge responses of small molecules containing the chemical functional groups of interest in modelling proteins. The approach is hierarchical, beginning with the fitting of aliphatic groups (methyl carbons, hydrogens, for instance), and then carrying these over into the determination of other groups. The electronegativities then are determined by fitting to charge distributions and dipole moments of isolated small molecules in vacuum.
A fictitious charge dynamics is performed in the spirit of Car-Parrinello or 'ab initio' molecular dynamics simulations. The charge sites are given masses (much smaller than the nuclei so as to maintain the system on the Born-Oppenheimer (BO) surface) and the entire system is propagated with an extened Lagrangian which enforces the required charge normalization. The charges are thermostatted to heat baths to maintain a relatively low temperature to ensure adiabaticity. Currently this is done via coupling to Nose-Hoover heat baths; groupings of charges can be separately coupled so as to avoid 'hot spots'.
# File: CHEQ, Node: Syntax, Up: Top, Previous: Description, Next: Options
Syntax of the CHEQ commands
CHEQ [ON ] [OFF ] [RESEt]
[NORM ] {BYRE | BYAL | BYSE | BYGP | BYMO} atom_selection
[QMAS ] CGMA {charge-mass} TSTA {initial temperature} atom_selection
[TIP4p] atom_selection [WATEr] [SPC ] [FLEX ]
CHEQ {WATE | SPC | FLEX} SELECT {selection} END
# File: CHEQ, Node: Options, Up: Top, Previous: Syntax, Next: Energy
CHEQ Command Options ON sets QCG flag to .TRUE. (turns on fluctuating charges). This can be issued anytime in order to switch between non-polarizable and polarizable Hamiltonians
OFF sets QCG flag to .FALSE. (turns off fluctuating charges). This can be issued anytime in order to switch between non-polarizable and polarizable Hamiltonians.
RESE turns off CHEQ (QCG=.FALSE.) and resets some CHEQ arrays and parameters as follows:
The variable 'QNPART' is set to zero (nullifies CHEQ normalization units; the user will have to respecify these with 'CHEQ NORM norm-option atom-selection as discussed under the 'NORM' option command.
QCG is set to FALSE; thus, ENERGY, MINIMIZATION, and DYNAMICS using the CHEQ method is no longer possible unless the CHEQ option us used with the relevant commands.
All arrays associated with the partitions, partition counters, and pointers to atoms of partitions are zeroed.
NORM sets up partitions for charge normalization. Implemented by setting total charge force for a partition to zero. Format for command: CHEQ NORM {BYRE | BYAL | BYSE | BYGP | BYMO} SELECT {selection} END description of options: BYRE - charge constant within residues in the given selection BYAL - charge constant within all atoms in the given selection BYSE - charge constant within segments in the given selection BYGR - charge constant within groups in the given selection BYMO - charge constant within molecules in the given selection NOFQ - turns off CHEQ for selected atoms
QMAS sets up mass and initial temperature for charges
QMAS CGMA {charge-mass} TSTA {initial temperature} {atom selection}
TIP4 selects the TIP4P-FQ water model of Rick and Berne Note: Consult the LONEPAIR documentation for properly setting up the constructs necessary to implement this 4-point water model and/or check the testcases
WATE Rigid water, derivatives of intra-molecular hardness elements with respect to coordinates are not computed.
SPC selects rigid 3-point water using special SPC parameters of Rick and Berne
FLEX generic CHEQ molecule type (flexible molecule; charge force on nuclei computed). The above options (WATE, SPC and FLEX, TIP4) are used similarly to the NORM command:
CHEQ {WATE | SPC | FLEX} SELECT {selection} END
PRIN Prints out several variables and arrays for CHEQ WALP sets parameters for restraint potential to bound charges on atoms; this is to prevent over-polarization in cases where the charges sample regions further away from the minimum determined by the quadratic form of the CHEQ potential. At this time, only two forms of the restraint are supported. Can be extended in the future.
For PTYP = 1 :
CHEQ WALP { PTYP integer} { QRQ1 real } { QRQ2 real } { QRK real } - atom_selection
For PTYP = 2 :
CHEQ WALP { PTYP integer} { WALN integer } - { QRA1 real } { QRAB1 real } { QRA2 real } { QRB2 real } - { QRQ1 real } { QRQ2 real } { QRK real } atom_selection
PTYP sets the type of restraint potential; 1=harmonic, 2=Nth order wall potential with switch. (Ref #)
QRQ1 the upper limit of the values a certain charge can take QRQ2 the lower limit of the values a certain charge can take QRK the force constant for harmonic restraint or the strength for the wall potential (generally on the order of 10**2)
The following are further specifications needed for a non-harmonic wall potential.
WALN integer value setting the hardness of the wall potential QRA1 charge value below which switching function is zero QRB1 charge value above which switching function is unity ** QRA1 < QRB1
QRA2 charge value above which switching function is zero QRB2 charge value below which switching function is unity ** QRA2 < QRB2
# File: CHEQ, Node: Energy, Up: Top, Previous: Options, Next: Scalar
Energy and Dynamics
CHEQ can be used with ENERgy, MINImization, and DYNAmics commands. Currently, minimization routines supporting CHEQ are the CONJugate gradients and STEEPest descents. For DYNAmics, the leapfrog integrator includes charge dymamics.
For these functions, the CHEQ flag must be specified so that the appropriate subroutines are used:
ENERGY energy_options CHEQ CHEQ_options
DYNA dynamics_options CHEQ CHEQ_options
MINI minimization_options CHEQ CHEQ_options where CHEQ_options are as in the following.
NOCO sets QNOCO flag to .TRUE. Freezes coordinates by zeroing DX,DY and DZ resets to .FALSE. when exiting ENERgy, MINImization, or DYNAmics call. Useful for minimizing charge for a fixed conformation. For a large system this can be faster than CGIN since the charges tend to converge rapidly.(<100 steps for 216 water system)
CGMD Used with ENERgy, MINIimization, and DYNAmics calls
int - 0 for normal Hamiltonian with exclusion in elec.interactions (default) 1 using Hamiltonian without exclusions (Recommended for FLUQ)
CGIN Used with ENERgy call
charges will be calculated by matrix inversion whenever energy is called. (WARNING: it is slow and memory intensive on big systems) This option does not work with IMAGES.(but does work with BOUND) This keyword must be specified every time it is wanted as the flag CGINV is set to .FALSE. after the command is performed.
POLT Used with ENERgy call
calculates the components of the molecular polarizability tensor based on the molecular geometry and hardness matrix elements. Used in conjunction with the ENERGY call.
Use care when comparing to experimental data; usually need to make sure that the same molecular orientations are being compared (i.e, planar water case, depending on the orientation, will get different results for the tensor component values).
FQPA Prints out the Eta matrix when doing matrix inversion. (i.e. only works in conjunction with CGIN keyword) This is an NATOM by NATOM array so can get very large. Flag resets to .FALSE. after command has executed.
FQINT used with DYNAmics call
sets the charge integration algorithm 1 = Nose-Hoover Temperature Control ** 2 = No temperature control required as input; default does not do charge dynamics
** Note: To use the Nose-Hoover algorithm for propagating the charge dynamics with temperature control, one must specify the degrees of freedom which are to be coupled to a given bath. The method for specifying this is similar to the multi-heat bath calls for the NOSE command to thermostat the nuclear degrees of freedom. The following command must be issued before the call to DYNAMICS:
FQBA I CALL J atom-selection-option COEF J QREF (0.005) TREF (1.0) . . . . END
The integer 'I' indicates the number of baths for groupings of charge degrees of freedom. For each bath, the 'CALL' and 'COEF' commands set the atoms coupled to that bath, the Nose-Hoover fictitious mass, QREF, for that bath, and the temperature, TREF, for that bath.
** CHEQ computation now turns on and off with SKIPE command. Tied to ELEC keyword. If SKIPE ELEC command is given CHEQ energy and derivatives are set to zero.
# File: CHEQ, Node: Scalar, Up: Top, Previous: Energy, Next: Example
SCALAR Command
The charge array has always been available from the scalar command, but there are now additional arrays specific to Fluc-Q that are accessible, namely the charge derivatives as well as both the eta and chi parameters. The keynames that have been added are:
DCH - charge derivatives EHA - hardness parameters for every atom ECH - electronegativity parameters for every atom
See the description of the * scalar command: (chmdoc/scalar.doc). for useage.
For information regarding variables used in conjunction with the CHEQ method, consult the include files cheqdyn.fcm and derivq.fcm in the source/fcm diretory.
# File: CHEQ, Node: Example, Up: Top, Previous: Scalar, Next: Mixed
Examples
There are examples of many of the commands described above in the test input script that is in the test/c30test directory. After the structure has been generated the CHEQ options can be set up. A typical sequence of commands might go something like:
{read RTF} ! read appropriate file to obtain CHEQ parameters; ! treated analogous to charges {read standard parameters}
{read sequence} GENErate
CHEQ norm byre select all end ! normalization over residues CHEQ flex select all end ! Flexible molecules energy cheq cgmd 1
# File: CHEQ, Node: Mixed, Up: Top, Previous: Example, Next: References
The CHEQ module currently allows one to simulate systems where some segments are polarizable and others are not (non-polarizable ion in polarizable solvent, see Example in this section). This set-up is referred to as FQ/MM by analogy to QM/MM methods (since the polarizable region allows for electronic response to local chemical environment). The algorithmically, the code checks whether atoms are assigned to a charge normalization unit (required for CHEQ minimization and dynamics); those charge on atoms which are not implicated in a specified charge normalization scheme are not propagated dynamically nor are they varied in minimization. In the case of mixed systems, the E14FAC parameter is not required to be set explicitly in the operating input script. The associated parameter file should use the default value of "1"; the code automatically allows for inclusion of 1-4 electrostatic interactions within the CHEQ formalism without any user input. The following is an example of setting up a mixed system of polarizable solvent (TIP4P-FQ) solvating a non-polarizable ion (sodium). The polarizability of the ion is effectively turned off by not specifying a normalization scheme for the non- polarizable solute (see also the test case /c32test/nawat.inp).
Example: box of 215 TIP4P-FQ water molecules solvation a single, NON-POLARIZABLE SODIUM ION
# read rtf and paramater files as usual read sequ tip4 215 generate wat first none last none setup noang nodihed read sequence sod 1 generate ion first none last none setup noang nodihed open read unit 1 form name @0tip4p_sod.crd read coor card unit 1 close unit 1 coor copy comp lonepair bisector dist 0.15 angle 0.0 dihe 0.0 - sele atom wat * OM end - sele atom wat * OH2 end - sele atom wat * H1 end - sele atom wat * H2 end
! *** To exclude the ion from having polarizability, note that it is assigned ! to no normalization unit. ***
CHEQ norm byres sele segid wat end CHEQ tip4 sele segid wat end CHEQ QMAS CGMA 0.000069 TSTA 0.01 sele segid wat end CHEQ NORM NOFQ SELE SEGID ION END ! ******
The last line above signifies that the sodium ion (treated as a segment here) will be treated as a fixed-charge entity.
# File: CHEQ, Node: References, Up: Top, Previous: Mixed, Next: Top References
1. Parr, R. G., and W. Yang. Density-Functional Theory of Atoms and Molecules. 1989. Oxford: Oxford University Press.
2. Sanderson, R. T. "Chemical Bonds and Bond Energy". 2nd. Edition, 1976, New York, Academic.
3. Sanderson, R. T. Science. 114. 1951, p.670.
4. Rick, S. W., S. J. Stuart, B. J. Berne. J. Chem. Phys. 101(7). 1994 pp.6141-6156.
5. Rick, S. W. and B. J. Berne. JACS. 118, 1996. pp672-679.
6. Mortier, W. J., S. K. Ghosh, S. Shankar. JACS. 108, 1986. pp.4315-4320.
7. Mortier, W. J., K. V. Genechten, and J. Gasteiger. JACS. 107, 1985. pp.829-835.
8. Rappe, A. K. and W. A. Goddard, III. J. Phys. Chem. 95, 1991. pp.3358-3363.
9. York, D. M. and W. Yang. J. Chem. Phys. 104(1), 1996. p.159.
10. Car. R, and M. Parrinello. Phys. Rev. Lett. 55, 1985. p.2471.
11. Blochl, P. E., and M. Parrinello. Phys. Rev. B. 45(16), 1992. p.9413.
12. Yoshii, N., R. Miyauchi, S. Miura, S. Okazaki. Chem. Phys. Lett. 317, 2000. pp.414-420.
13. Naleewajski, R. F., J. Korchowiec, and Z. Zhou. Int. J. Quant. Chem. Quantum Chemistry Symposium 22, 1988. pp.349-366.
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Combined QM/MM Fluctuating Charge Potential for CHARMM
Ben Webb, [email protected], and Paul Lyne
The fluctuating charge potential (FlucQ or FQ) is based on the method developed by Rick, Stuart and Berne (Rick et. al., J. Chem. Phys. 101 (7) 1994 p6141) for molecular dynamics, and extended for hybrid QM/MM simulations (Bryce et. al., Chem. Phys. Lett. 279 1997, p367). It is designed primarily for computationally efficient (approx. 10% overhead) modelling of solvent polarisation in hybrid QM/MM systems, and as such is implemented for QUANTUM, CADPAC and GAMESS codes, although the current implementation is easily extensible to any atom type and bond.
* Menu:
* Syntax:: Syntax of the FLUCQ command * Activation:: Starting FlucQ from a CHARMM input file * Charge solution:: Solving for exact charges * Reference energy:: Setting the ``zero'' for FlucQ polarisation * Caveats:: Changes to be aware of; known limitations * Using FlucQ with QM:: Necessary changes for use with CADPAC or GAMESS * Examples:: Simple uses of the FLUCQ command * Implementation:: Mathematical and computational details
# File: flucq, Node: Syntax, Next: Activation, Prev: Top, Up: Top
[SYNTAX FLUCq]
FLUCq { ON init-spec (atom selection) } { OFF } { PRINt } { EXACt exac-spec } { REFErence { GAS exac-spec } } { { SOLVent exac-spec } } { { CURRent } } { { ENERgy real } }
DYNAmics ... thermo-spec
init-spec::= [GROUp] [NOFIxed]
exac-spec::= [TIMEstep real] [ZETA real] [TQDEsired real] [PRINt]
thermo-spec::= [FQTEmp real] [FQUNit integer] { FQTCoupling real } ! weak coupling { FQMAss real nose-spec } ! Nose-Hoover { FQSCale integer } ! velocity scaling
nose-spec::= [FQTOlerance real] [FQITerations integer]
# File: flucq, Node: Activation, Next: Charge solution, Prev: Syntax, Up: Top FlucQ code is enabled within CHARMM by means of the FLUCQ ON command. Future energy calculations will then include an extra energy term - FQPO, the FlucQ polarisation energy, while dynamics simulations involve a new energy property - FQKI, the FlucQ charge kinetic energy. Once FlucQ is active, the selected atoms are treated as extra degrees of freedom, free to fluctuate under the charge forces in the system, and, by assigning each atom type a fictional charge "mass", these charges can be accelerated in a conventional dynamics simulation, in a completely analogous way to the Cartesian degrees of freedom.
If atoms are selected by the FLUCQ command which cannot be modelled (i.e. they are QM atoms, or have no FlucQ parameters defined for them) they will be automatically removed from the selection.
The FlucQ polarisation energy, FQPO, is an intramolecular interaction; in full electronegativity equalisation, every atom interacts through space, by means of a modified Coulomb-type interaction, with every other atom in the molecule. In this implementation, the only interactions calculated are those along defined CHARMM bonds (even those with zero force constants).
[GROUp] conserves charge within groups, rather than the default behaviour of conserving charge within residues; this prohibits charge transfer between groups. Note that the FlucQ model makes no restriction on the degree of charge transfer within each residue or group, or the distance over which this transfer can occur.
[NOFIxed] instructs FlucQ that some or all of the bond lengths between FlucQ- selected atoms are free to change during a simulation. This forces the FlucQ code to recalculate the intramolecular interaction at each step; since this is a costly calculation, the default is to use interactions parameterised for equilibrium bond lengths, with which it is strongly recommended to combine constraint methods such as SHAKE BONH PARA.
The FLUCq PRINt command simply prints the current values of all charges and charge forces (from the last energy calculation). A similar effect can also be achieved with the standard SCALAR command (see scalar.doc for information on other FlucQ parameters available with the SCALAR command).
The FLUCQ OFF command disables the FlucQ code. Further energy calculations will not include FlucQ terms. Note, however, that if the charges have been modified by FlucQ, they will remain at their altered values.
Default behaviour during dynamics is to allow the charge degrees of freedom to fluctuate freely; however they can be thermostatted at a given charge "temperature" by passing extra options to the DYNAmics command:-
[FQTEmp
[FQTCoupling
[FQMAss
Thermostatting parameters (number of iterations, scale factor, etc.) can be written out to a given unit number at every dynamics step by using the FQUNit (default -1: no write) option. [FQSCal
The initialization process dimensions FlucQ with the current state of the system. The QM region, if any, is detected, and the FlucQ atom selection will then interact with the QM region. Thus, the FLUCQ command should be placed after any QUANTUM, CADPAC, or GAMESS command, and if the total number of atoms in the system is modified, FlucQ should be disabled prior to this change and reinitialized afterwards.
To skip FlucQ energy calculations entirely, use the SKIP FQPOL FQKIN command. The QM/MM FlucQ interaction is calculated in line with the standard QM/MM electrostatic interaction, and as such is suppressed with the SKIP QMEL command. Finally, the intermolecular contribution to FlucQ is calculated in line with the standard electrostatic interaction, and so is disabled with the SKIP ELEC command.
No FlucQ interaction energies are calculated between atoms constrained with the CONS FIX command, as electrostatic energies are not calculated for these atoms.
FlucQ parameters are specified in the parameter file, with the FLUCQ keyword. The section should look like the following:-
FLUCQ atom chi zeta prin mass
Here, chi is an electronegativity measure (in Kcal/mol/e), zeta a Slater orbital exponent (in 1/Angstrom), prin the Slater orbital principal quantum number, and mass the charge mass (in (ps/e)**2 Kcal/mol) from the FlucQ model. For example, Rick's original parameters for TIP4P hydrogen and M-site would be written as:-
FLUCQ HP 10.00 0.90 1 6.0d-5 MP 78.49 1.63 2 6.0d-5
# File: flucq, Node: Charge solution, Next: Reference energy, Prev: Activation, Up: Top
The FlucQ model relies on keeping charge kinetic energy at a temperature close to zero Kelvin, to maintain Born-Oppenheimer separation between it and the other degrees of freedom. Thus, it is best to acquire a minimum energy charge configuration for your system before any dynamics simulation.
Two methods are available for such "charge solution". The first is to use a standard CHARMM minimisation; FlucQ charges will be minimised concurrently with the Cartesian coordinates. The second method is to apply dissipative Langevin dynamics to the charges only, to achieve minimum energy charges for fixed atomic coordinates; this is performed by means of the FLUCq EXACt command. The code prints a running count of the number of iterations required to quench the kinetic energy.
[TIMEstep real] sets the timestep to be used in Langevin dynamics, by default 0.001ps.
[ZETA real] sets the frictional coefficient, by default 1600.
[TQDEsired real] sets the desired final temperature, by default 1.0d-6 K.
[PRINt] if set, prints the final charges.
# File: flucq, Node: Reference energy, Next: Caveats, Prev: Charge solution, Up: Top
By default, the charge polarisation energy FQPOL reported by FlucQ is given relative to all atomic charges being zero. More generally, it is useful to define this term relative to an arbitrary zero. This reference energy can be set with the FLUCQ REFErence command.
FLUCQ REFE GAS disables all intermolecular interactions, solves for exact charges, and then uses the resultant energy as the reference. This essentially defines the polarisation energy relative to the energy that the system would have in the gas phase, with all residues or groups infinitely separated.
FLUCQ REFE SOLVENT merely disables the QM/MM interaction, and then sets the reference energy similarly. This shows polarisation as a function purely of the QM system.
FLUCQ REFE CURRent defines the current polarisation energy (from the last energy calculation) to be zero - i.e. the reference energy is increased by the current energy.
FLUCQ REFE ENERgy real sets the reference energy to a user-specified value.
Bear in mind that REFE GAS exac-spec is essentially identical to the series of CHARMM commands:-
FLUCQ REFER ENER 0 SKIP ALL EXCL FQPOL BOND ANGL UREY DIHE IMPR FLUCQ EXACT exac-spec FLUCQ REFER ENER ?FQPO SKIP EXCL ALL
(The only difference is that any SKIP command in force before REFE GAS will remain in force afterwards, whereas the above example will re-include calculation of all energy terms at completion. Also, by changing the second line in the above example to SKIP QMEL QMVDW, the action of the REFE SOLVENT command can be reproduced.)
# File: flucq, Node: Caveats, Next: Using FlucQ with QM, Prev: Reference energy, Up: Top
The fluctuating charge code alters the atomic charges during dynamics runs. Thus, the charges cannot be treated as constant and restart and trajectory files must include atomic charges. Files read or written during FlucQ-enabled dynamics runs will be assumed to contain charge information, and so will be a) somewhat larger and b) incompatible with non-FQ files. (If FlucQ is compiled in but not activated with FLUCQ ON, the restart and trajectory file formats are unchanged from standard CHARMM.)
The FlucQ model is implemented primarily for the study of QM/MM systems, with a fluctuating charge SHAKE-constrained MM solvent. Hence, intramolecular interactions are restricted to those between FlucQ atoms along bonds. This complicates the application of the model to large systems, as for full electronegativity equalisation, every atom must interact with every other atom in the group.
FlucQ is not implemented for all nonbond routines, in particular the CFF, MMFF, CRAYVEC and PARVECT codes. FlucQ also works only with standard Ewald, and not PME.
# File: flucq, Node: Using FlucQ with QM, Next: Examples, Prev: Caveats, Up: Top
In order for the QM/MM calculation to be properly calculated, FlucQ requires data to be passed back to it from the QM codes (in particular the density matrix and one-electron integrals). Changes have been made to the QUANTUM interface for this to be carried out correctly; however, the GAMESS(US) and CADPAC codes, not being distributed with CHARMM, will require modification. These modifications will not affect the functioning of standard QM/MM calculations, when FlucQ is disabled. GAMESS-UK (versions 6.3.1 and later) should incorporate the required modifications.
Patches for GAMESS(US), and CADPAC can be found in the source/flucq/ directory in the main CHARMM distribution. They should be applied in the top directory of the relevant QM code distributionm i.e. gamess-us.patch and cadpac.patch should be applied in the source/gamint/gamess/ and source/cadint/cadpac/ directories, respectively. The patch files are standard unified diffs, and so should be applied with a command similar to "patch -p1 < gamess-us.patch"
# File: flucq, Node: Examples, Next: Implementation, Prev: Using FlucQ with QM, Up: Top
The following example initialises the FlucQ code for a system of SPC waters, before calculating the gas phase energy, and then calculating the self-polarisation of the solvent. Finally, the total energy, including the self-polarisation relative to the gas phase, is printed, and the charge forces from this energy calculation are displayed.
FLUCQ ON SELE RESN SPC END FLUCQ REFER GAS FLUCQ EXACT ENERGY SCALAR FQCFOR SHOW SELE ALL END
See the testcase test/c28test/fqam1.inp for an example of a FlucQ dynamics simulation.
# File: flucq, Node: Implementation, Prev: Examples, Up: Top
The standard CHARMM nonbond routines and QM codes have been modified so as to sum the interaction electrostatic interaction energy between charge "I" and all other nonbond pairs or QM atoms into index "I" of the fluctuating charge array FQCFOR. The FlucQ model actually requires the term dE/dQ, so these totals are divided by charge by the FlucQ energy routine (as all such interactions are linear in charge). Note that this gives erroneous results for FlucQ sites with exactly zero charge; however, the CHARMM nonbond routines calculate no interactions for such systems anyway.
Finally, the intramolecular terms, as contributions to dE/dQ, are summed into the FQCFOR array, and charge forces are calculated from these electronegativities by mass-weighted averaging over residues or groups. These forces are then used by the standard minimisers, or by a standard Verlet integrator during dynamics. For further information, see the following:- MM system; (Rick et. al., J. Chem. Phys. 101 (7) 1994 p6141) QM/MM interaction; (Bryce et. al., Chem. Phys. Lett. 279 1997, p367)
# Tag Table: Node: Top103 Node: Syntax1371 Node: Activation2114 Node: Charge solution6634 Node: Reference energy7793 Node: Caveats9466 Node: Using FlucQ with QM10631 Node: Examples15843 Node: Implementation16424 # End Tag Table * QM/MM water dimer * bomlev -3 read rtf card * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19 * 20 1 ! Version number MASS 4 HT 1.00800 ! TIPS3P WATER HYDROGEN MASS 58 OT 15.99940 ! TIPS3P WATER OXYGEN RESI TIP3 .000 ! TIPS3P WATER MODEL GROUP ATOM OH2 OT -0.834 ATOM H1 HT 0.417 ATOM H2 HT 0.417 BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE ANGLE H1 OH2 H2 !ACCE OH2 IC H1 OH2 H2 BLN 0.0 0.0 0.0 0.0 0.0 IC H2 OH2 H1 BLN 0.0 0.0 0.0 0.0 0.0 PATC FIRS NONE LAST NONE end read param card * BOND HT OT 450.0 0.9572 ! from TIPS3P geometry HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) ANGLE HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY
NONBONDED NBXMOD 5 ATOM CDIEL SHIFT VATOM VDISTANCE VSHIFT - CUTNB 12.0 CTOFNB 10.5 CTONNB 9.0 EPS 1.0 E14FAC 0.4 WMIN 1.5 !
HT 0.0440 -0.0498 0.8000 !TIP3P water hydrogen, see NBFIX below OT 0.8400 -0.1591 1.6000 !TIP3P water oxygen, see NBFIX below
NBFIX ! Emin Rmin ! (kcal/mol) (A) ! ! We're gonna NBFIX the TIP3P water-water interactions ! here to make them more like Jorgensen's. The vdW parameters ! specified above will be in effect, therefore, for ONLY ! protein (read, protein OR nucleic acid)-water interactions. ! OT-OT is exactly Jorgensen's; HT interactions are added ! here. ! OT OT -0.152073 3.5365 ! TIPS3P VDW INTERACTION HT HT -0.04598 0.4490 HT OT -0.08363 1.9927 end read sequ card 2 TIP3 TIP3 generate W setup warn read coor card * WATER * DATE: 7/10/ 2 4:25:51 CREATED BY USER: hlwood * 6 1 1 TIP3 OH2 -1.30910 -0.25601 -0.24045 W 1 0.00000 2 1 TIP3 H1 -1.85344 0.07163 0.52275 W 1 0.00000 3 1 TIP3 H2 -1.70410 0.16529 -1.04499 W 1 0.00000 4 2 TIP3 OH2 1.37293 0.05498 0.10603 W 2 0.00000 5 2 TIP3 H1 1.65858 -0.85643 0.10318 W 2 0.00000 6 2 TIP3 H2 0.40780 -0.02508 -0.02820 W 2 0.00000
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! envi qchemcnt "qchem.inp" envi qcheminp "q1.inp" envi qchemexe "qchem" envi qchemout "qchem.out" envi PBS_NODEFILE "qchost" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! qchem remove sele resid 2 show end energy coor force comp print coor comp stop * QM/MM water dimer * bomlev -3 read rtf card * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19 * 20 1 ! Version number MASS 4 HT 1.00800 ! TIPS3P WATER HYDROGEN MASS 58 OT 15.99940 ! TIPS3P WATER OXYGEN RESI TIP3 .000 ! TIPS3P WATER MODEL GROUP ATOM OH2 OT -0.834 ATOM H1 HT 0.417 ATOM H2 HT 0.417 BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE ANGLE H1 OH2 H2 !ACCE OH2 IC H1 OH2 H2 BLN 0.0 0.0 0.0 0.0 0.0 IC H2 OH2 H1 BLN 0.0 0.0 0.0 0.0 0.0 PATC FIRS NONE LAST NONE end read param card * BOND HT OT 450.0 0.9572 ! from TIPS3P geometry HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) ANGLE HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY
NONBONDED NBXMOD 5 ATOM CDIEL SHIFT VATOM VDISTANCE VSHIFT - CUTNB 12.0 CTOFNB 10.5 CTONNB 9.0 EPS 1.0 E14FAC 0.4 WMIN 1.5 !
HT 0.0440 -0.0498 0.8000 !TIP3P water hydrogen, see NBFIX below OT 0.8400 -0.1591 1.6000 !TIP3P water oxygen, see NBFIX below
NBFIX ! Emin Rmin ! (kcal/mol) (A) ! ! We're gonna NBFIX the TIP3P water-water interactions ! here to make them more like Jorgensen's. The vdW parameters ! specified above will be in effect, therefore, for ONLY ! protein (read, protein OR nucleic acid)-water interactions. ! OT-OT is exactly Jorgensen's; HT interactions are added ! here. ! OT OT -0.152073 3.5365 ! TIPS3P VDW INTERACTION HT HT -0.04598 0.4490 HT OT -0.08363 1.9927 end read sequ card 2 TIP3 TIP3 generate W setup warn read coor card * WATER * DATE: 7/10/ 2 4:25:51 CREATED BY USER: hlwood * 6 1 1 TIP3 OH2 -1.30910 -0.25601 -0.24045 W 1 0.00000 2 1 TIP3 H1 -1.85344 0.07163 0.52275 W 1 0.00000 3 1 TIP3 H2 -1.70410 0.16529 -1.04499 W 1 0.00000 4 2 TIP3 OH2 1.37293 0.05498 0.10603 W 2 0.00000 5 2 TIP3 H1 1.65858 -0.85643 0.10318 W 2 0.00000 6 2 TIP3 H2 0.40780 -0.02508 -0.02820 W 2 0.00000
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! envi qchemcnt "qchem.inp" envi qcheminp "q1.inp" envi qchemexe "qchem" envi qchemout "qchem.out" envi PBS_NODEFILE "qchost" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! qchem remove sele resid 2 show end energy coor force comp print coor comp stop m1(6-31G_D)% m1(6-31G_D)% c m1(6-31G_D)% cat output.dat 0 process started 1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 32a2 February 15, 2005 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.4.20-42.7.legacysmp(i686)@m1.lobos.n Created on 3/21/ 6 at 0:14:59 by user: hlwood
Maximum number of ATOMS: 240480, and RESidues: 60120 Current HEAP size: 10240000, and STACK size: 2000000
RDTITL> * QM/MM WATER DIMER RDTITL> *
CHARMM>
CHARMM> bomlev -3
CHARMM> CHARMM> read rtf card MAINIO> Residue topology file being read from unit 5. RDTITL> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19 RDTITL> *
CHARMM>
CHARMM> read param card
PARAMETER FILE BEING READ FROM UNIT 5 RDTITL> * RDTITL> No title read. PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM>
CHARMM> read sequ card MAINIO> Sequence information being read from unit 5. RDTITL> 2 RDTITL> No title read.
SEQRDR> 2
SEQRDR> TIP3 TIP3
RESIDUE SEQUENCE -- 2 RESIDUES TIP3TIP3
CHARMM> generate W setup warn NO PATCHING WILL BE DONE ON THE FIRST RESIDUE NO PATCHING WILL BE DONE ON THE LAST RESIDUE GENPSF> Segment 1 has been generated. Its identifier is W. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 2 Number of atoms = 6 Number of groups = 2 Number of bonds = 6 Number of angles = 2 Number of dihedrals = 0 Number of impropers = 0 Number of cross-terms = 0 Number of HB acceptors = 0 Number of HB donors = 0 Number of NB exclusions = 0 Total charge = 0.00000
CHARMM>
CHARMM> read coor card SPATIAL COORDINATES BEING READ FROM UNIT 5 RDTITL> * WATER RDTITL> * DATE: 7/10/ 2 4:25:51 CREATED BY USER: HLWOOD RDTITL> *
CHARMM>
CHARMM>
CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> envi qchemcnt "qchem.inp"
CHARMM> envi qcheminp "q1.inp" CHARMM> envi qchemexe "qchem"
CHARMM> envi qchemout "qchem.out"
CHARMM> envi PBS_NODEFILE "qchost"
CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM>
CHARMM> qchem remove sele resid 2 show end The following atoms are currently set: SEGId RESId RESName .. TYPEs .. W 2 TIP3 OH2 H1 H2 SELRPN> 3 atoms have been selected out of 6 QCHEM> REMOve: Classical energies within QM atoms are removed. QCHEM> No EXGRoup: QM/MM Elec. for link atom host only is removed. QCHEM> No QINP: Charges will be based on atomic numbers. ------QCHEM: Classical atoms excluded from the QM calculation: NONE. QCHEM: Quantum mechanical atoms: 4 W 2 TIP3 OH2 5 W 2 TIP3 H1 6 W 2 TIP3 H2 QCHEM: Quantum mechanical link atoms: NONE. ------
CHARMM>
CHARMM> energy
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSHIft BYGRoup NOEXtnd NOEWald CUTNB = 12.000 CTEXNB =999.000 CTONNB = 9.000 CTOFNB = 10.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 0.400 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions.
General atom nonbond list generation found: 9 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
QCHEM> QCHEM> Q-Chem Job Parameters QCHEM> ------QCHEM> exchange hf QCHEM> basis 6-31g* QCHEM> FINDEL: Quantum atom 4 W 2 TIP3 OH2 assigned to element: O 8 FINDEL: Quantum atom 5 W 2 TIP3 H1 assigned to element: H 1 FINDEL: Quantum atom 6 W 2 TIP3 H2 assigned to element: H 1 ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ENER QUANTUM: QMELec QMVDw ------ENER> 0 -47703.60556 0.00000 13.50059 ENER INTERN> 1.07269 0.01264 0.00000 0.00000 0.00000 ENER EXTERN> 2.06484 0.00000 0.00000 0.00000 0.00000 ENER QUANTM> -47706.75573 0.00000 ------
CHARMM>
CHARMM> coor force comp SELECTED FORCES COPIED TO THE COMPARISON SET.
CHARMM> print coor comp
COORDINATE FILE MODULE TITLE> * QM/MM WATER DIMER TITLE> * 6 1 1 TIP3 OH2 18.46113 -20.41920 -1.41965 W 1 0.00000 2 1 TIP3 H1 -12.32710 8.40684 23.84753 W 1 0.00000 3 1 TIP3 H2 -6.88229 10.35089 -22.60745 W 1 0.00000 4 2 TIP3 OH2 19.67340 14.29671 3.35581 W 2 0.00000 5 2 TIP3 H1 -0.40946 -10.26245 -0.49653 W 2 0.00000 6 2 TIP3 H2 -18.51568 -2.37279 -2.67971 W 2 0.00000
CHARMM>
CHARMM> stop Parallel load balance (sec.): Node Eext Eint Wait Comm List Integ Total 0 0.0 1.9 0.0 0.0 0.0 0.0 1.9
$$$$$$ New timer profile Local node$$$$$
Electrostatic & VDW 0.00001 Other: 0.00000 Nonbond force 0.00007 Other: 0.00005 Bond energy 0.00002 Other: 0.00000 Angle energy 0.00002 Other: 0.00000 Dihedral energy 0.00001 Other: 0.00000 Restraints energy 0.00000 Other: 0.00000 INTRNL energy 1.85695 Other: 1.85690 Comm force 0.00001 Other: 0.00000 Energy time 1.85706 Other: 0.00003 Total time 1.93127 Other: 0.07422
$$$$$$ Average profile $$$$$
Electrostatic & VDW 0.00001 Other: 0.00000 Nonbond force 0.00007 Other: 0.00005 Bond energy 0.00002 Other: 0.00000 Angle energy 0.00002 Other: 0.00000 Dihedral energy 0.00001 Other: 0.00000 Restraints energy 0.00000 Other: 0.00000 INTRNL energy 1.85695 Other: 1.85690 Comm force 0.00001 Other: 0.00000 Energy time 1.85706 Other: 0.00003 Total time 1.93127 Other: 0.07422
NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 60120 STACK CURRENTLY IN USE IS 0 NO WARNINGS WERE ISSUED HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 0 MAXIMUM SPACE USED IS 4504 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0
$$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 1.93 SECONDS CPU TIME: 0.08 SECONDS * CHARMM / Q-Chem Testcase cquantumtest/alanine_qchem.inp * Author: Paul Sherwood (Modifed for Q-Chem by H. Lee Woodcock) * Alalnine test case for QM(Q-Chem)/MM using Q-Chem interface * CTERM is QM and the rest is MM Link atom is between CA and C * Runs ~ 3 min on HP-735 * Requires alanine_qchem.in * if ?qchem .ne. 1 then stop STREam datadir.def read rtf card * Taken from top_all22_prot.inp * 22 1 MASS 1 H 1.00800 ! polar H MASS 2 HC 1.00800 ! N-ter H MASS 3 HA 1.00800 ! nonpolar H MASS 6 HB 1.00800 ! backbone H MASS 20 C 12.01100 ! polar C MASS 22 CT1 12.01100 ! aliphatic sp3 C for CH MASS 24 CT3 12.01100 ! aliphatic sp3 C for CH3 MASS 32 CC 12.01100 ! carbonyl C for sidechains asn,asp,gln,glu MASS 54 NH1 14.00700 ! peptide nitrogen MASS 56 NH3 14.00700 ! ammonium nitrogen MASS 70 O 15.99900 ! carbonyl oxygen MASS 72 OC 15.99900 ! carboxylate oxygen mass 9 QQH 1.00800 ! link atom
DECL -CA DECL -C DECL -O DECL +N DECL +HN DECL +CA
DEFA FIRS NTER LAST CTER AUTO ANGLES DIHE
RESI ALA 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB2 ATOM CB CT3 -0.27 ! | \ ATOM HB1 HA 0.09 ! | HB3 ATOM HB2 HA 0.09 ! O=C ATOM HB3 HA 0.09 ! | GROUP ! ATOM C C 0.51 ATOM O O -0.51 BOND CB CA N HN N CA O C BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114
PRES CTER -1.00 ! standard C-terminus GROUP ! use in generate statement ATOM C CC 0.34 ! OT2 ATOM OT1 OC -0.67 ! // ATOM OT2 OC -0.67 ! -C DELETE ATOM O ! \\ BOND C OT1 C OT2 ! OT1 IMPR OT1 CA OT2 C ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
PRES NTER 1.00 ! standard N-terminus GROUP ! use in generate statement ATOM N NH3 -0.30 ! ATOM HT1 HC 0.33 ! HT1 ATOM HT2 HC 0.33 ! / ATOM HT3 HC 0.33 ! --CA--N--HT2 ATOM CA CT1 0.21 ! | \ ATOM HA HB 0.10 ! HA HT3 DELETE ATOM HN BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 end read param card * from par_all22_prot.inp *
BONDS CT1 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 HC 403.000 1.0400 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION ! adm jr. 7/23/91, acetic acid NH3 CT1 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) CT3 CT1 222.500 1.5380 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 322.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HB CT1 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) qqh cc 0.0 1.0 ! Link atom
ANGLES NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 HC 44.000 109.5000 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/09/92, for ALA cter NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HB CT1 CT3 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP ! new aliphatics, adm jr., 2/3/92 OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO ! adm jr. 7/23/91, correction, ACETATE (KK) qqh cc ct1 0.0 0.0 ! Link atom
DIHEDRALS OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO ! adm jr. 4/17/94, zwitterionic glycine X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL ! 0.715->0.10 METHYLAMMONIUM (KK) X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
IMPROPER OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION ! 90.0->96.0 acetate, single impr (KK)
NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - cutnb 13.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO ! NMA pure solvent, adm jr., 3/3/93 CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO ! adm jr. 3/3/92, acetic acid heat of solvation CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! isobutane pure solvent properties, adm jr, 2/3/92 CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC ! same as TIP3P hydrogen, adm jr., 7/20/89 HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HC 0.000000 -0.046000 0.224500 ! ALLOW POL ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) NH3 0.000000 -0.200000 1.850000 ! ALLOW POL ! adm jr. O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION ! JG 8/27/89 qqh 0.000000 0.000000 0.000000 ! Link atom end read sequ ala 1 gene mpep setup ic param ic seed mpep 1 n mpep 1 ca mpep 1 c ic build mini abnr nstep 1000 nprint 1000 addl qqh1 mpep 1 c mpep 1 ca
!------Needed to define Q-Chem env. vars. ------envi qchemcnt "data/qchem.inp" envi qcheminp "q1.inp" envi qchemexe "qchem" envi qchemout "qchem.out" !------define qm sele atom mpep 1 c .or. atom mpep 1 ot1 - .or. atom mpep 1 ot2 end qchem remove sele qm end open write card unit 1 name @9/test.psf write psf card unit 1 * after qchem * open write card unit 1 name @9/test.coor write coor card unit 1 * after qchem * energy open write card unit 1 name @9/test2.psf write psf card unit 1 * after qchem * open write card unit 1 name @9/test2.coor write coor card unit 1 * after qchem * scal xcomp = x scal ycomp = y scal zcomp = z scal x = dx scal y = dy scal z = dz open write card unit 1 name @9/test2.frc write coor card unit 1 * forces after qchem *
! restore forces scal x = xcomp scal y = ycomp scal z = zcomp test first tol 0.0 step 0.0005 stop 1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 33a2 February 15, 2006 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.4.20-28.9smp(i686)@n190.lobos.nih.go Created on 3/21/ 6 at 0:19:17 by user: hlwood
Maximum number of ATOMS: 240480, and RESidues: 80160 Current HEAP size: 10240000, and STACK size: 10000000
Processing passed argument "-p4wd" RDTITL> * CHARMM / Q-CHEM TESTCASE CQUANTUMTEST/ALANINE_QCHEM.INP RDTITL> * AUTHOR: PAUL SHERWOOD (MODIFED FOR Q-CHEM BY H. LEE WOODCOCK) RDTITL> * ALALNINE TEST CASE FOR QM(Q-CHEM)/MM USING Q-CHEM INTERFACE RDTITL> * CTERM IS QM AND THE REST IS MM LINK ATOM IS BETWEEN CA AND C RDTITL> * RUNS ~ 3 MIN ON HP-735 RDTITL> * REQUIRES ALANINE_QCHEM.IN RDTITL> *
CHARMM>
CHARMM> if ?qchem .ne. 1 then stop RDCMND substituted energy or value "?QCHEM" to "1" Comparing "1" and "1". IF test evaluated as false. Skipping command
CHARMM> STREam datadir.def VOPEN> Attempting to open::datadir.def:: OPNLGU> Unit 99 opened for READONLY access to datadir.def
INPUT STREAM SWITCHING TO UNIT 99 RDTITL> * CHARMM TESTCASE DATA DIRECTORY ASSIGNMENT RDTITL> * Parameter: IN1 <- ""
CHARMM> faster on MISCOM> FAST option: EXPANDED (limited fast routines)
CHARMM> set 0 data/ ! input data directory Parameter: 0 <- "DATA/"
CHARMM> set 9 scratch/ ! scratch directory Parameter: 9 <- "SCRATCH/"
CHARMM> return VCLOSE: Closing unit 99 with status "KEEP"
RETURNING TO INPUT STREAM 5
CHARMM>
CHARMM> read rtf card MAINIO> Residue topology file being read from unit 5. RDTITL> * TAKEN FROM TOP_ALL22_PROT.INP RDTITL> *
CHARMM>
CHARMM> read param card
PARAMETER FILE BEING READ FROM UNIT 5 RDTITL> * FROM PAR_ALL22_PROT.INP RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM>
CHARMM> read sequ ala 1
CHARMM> gene mpep setup THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE GENPSF> Segment 1 has been generated. Its identifier is MPEP. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 1 Number of atoms = 13 Number of groups = 3 Number of bonds = 12 Number of angles = 21 Number of dihedrals = 24 Number of impropers = 1 Number of cross-terms = 0 Number of HB acceptors = 2 Number of HB donors = 3 Number of NB exclusions = 0 Total charge = 0.00000
CHARMM>
CHARMM> ic param
CHARMM> ic seed mpep 1 n mpep 1 ca mpep 1 c
CHARMM> ic build
CHARMM>
CHARMM> mini abnr nstep 1000 nprint 1000
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions.
General atom nonbond list generation found: 45 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
ABNER> An energy minimization has been requested. EIGRNG = 0.0005000 MINDIM = 5 NPRINT = 1000 NSTEP = 1000 PSTRCT = 0.0000000 SDSTP = 0.0200000 STPLIM = 1.0000000 STRICT = 0.1000000 TOLFUN = 0.0000000 TOLGRD = 0.0000000 TOLITR = 100 TOLSTP = 0.0000000 FMEM = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER ------MINI> 0 -32.94894 0.00000 8.35393 0.00000 MINI INTERN> 0.07799 0.71822 0.06446 0.02172 0.00000 MINI EXTERN> 3.07138 -36.90272 0.00000 0.00000 0.00000 ------UPDECI: Nonbond update at step 82 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 79 ATOM PAIRS AND 0 GROUP PAIRS
General atom nonbond list generation found: 45 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
ABNER> Minimization exiting with function tolerance ( 0.0000000) satisfied.
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ABNR EXTERN: VDWaals ELEC HBONds ASP USER ------ABNR> 434 -36.80908 3.86014 0.00000 0.00000 ABNR INTERN> 0.48093 2.50118 0.47296 1.79235 0.01040 ABNR EXTERN> 5.06122 -47.12813 0.00000 0.00000 0.00000 ------
CHARMM>
CHARMM> addl qqh1 mpep 1 c mpep 1 ca
Message from MAPIC: Atom numbers are changed. ADDLNAT: Link atom placed 1.00000 A from QM atom. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 1 Number of atoms = 14 Number of groups = 4 Number of bonds = 14 Number of angles = 22 Number of dihedrals = 24 Number of impropers = 1 Number of cross-terms = 0 Number of HB acceptors = 2 Number of HB donors = 3 Number of NB exclusions = 0 Total charge = 0.00000
CHARMM>
CHARMM> !------Needed to define Q-Chem env. vars. ------CHARMM> envi qchemcnt "data/qchem.inp"
CHARMM> envi qcheminp "q1.inp"
CHARMM> envi qchemexe "qchem"
CHARMM> envi qchemout "qchem.out"
CHARMM> !------CHARMM>
CHARMM> define qm sele atom mpep 1 c .or. atom mpep 1 ot1 - CHARMM> .or. atom mpep 1 ot2 end SELRPN> 3 atoms have been selected out of 14
CHARMM>
CHARMM> qchem remove sele qm end SELRPN> 3 atoms have been selected out of 14 QCHEM> REMOve: Classical energies within QM atoms are removed. QCHEM> No EXGRoup: QM/MM Elec. for link atom host only is removed. QCHEM> No QINP: Charges will be based on atomic numbers. ------QCHEM: Classical atoms excluded from the QM calculation: 5 MPEP 1 ALA CA QCHEM: Quantum mechanical atoms: 11 MPEP 1 ALA C 12 MPEP 1 ALA OT1 13 MPEP 1 ALA OT2 QCHEM: Quantum mechanical link atoms: 14 MPEP 1 ALA QQH1 ------
CHARMM>
CHARMM> open write card unit 1 name @9/test.psf Parameter: 9 -> "SCRATCH/" VOPEN> Attempting to open::scratch//test.psf:: OPNLGU> Unit 1 opened for WRITE access to scratch//test.psf
CHARMM> write psf card unit 1 RDTITL> * AFTER QCHEM RDTITL> *
CHARMM>
CHARMM> open write card unit 1 name @9/test.coor Parameter: 9 -> "SCRATCH/" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::scratch//test.coor:: OPNLGU> Unit 1 opened for WRITE access to scratch//test.coor
CHARMM> write coor card unit 1 RDTITL> * AFTER QCHEM RDTITL> * VCLOSE: Closing unit 1 with status "KEEP"
CHARMM>
CHARMM> energy
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions.
General atom nonbond list generation found: 51 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
QCHEM> QCHEM> Q-Chem Job Parameters QCHEM> ------QCHEM> exchange hf QCHEM> basis sto-3g QCHEM> FINDEL: Quantum atom 11 MPEP 1 ALA C assigned to element: C 6 FINDEL: Quantum atom 12 MPEP 1 ALA OT1 assigned to element: O 8 FINDEL: Quantum atom 13 MPEP 1 ALA OT2 assigned to element: O 8 FINDEL: Quantum atom 14 MPEP 1 ALA QQH1 assigned to element: QQH 1 EANGLFS> Warning: Angle 22 is almost linear. Derivatives may be affected for atoms: 14 11 5 ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ENER QUANTUM: QMELec QMVDw ------ENER> 0-116435.43164 116398.62256 37.37005 ENER INTERN> 0.40179 2.48726 0.47262 1.79235 0.00000 ENER EXTERN> 5.06122 2.30201 0.00000 0.00000 0.00000 ENER QUANTM> -116447.94890 0.00000 ------
CHARMM>
CHARMM> open write card unit 1 name @9/test2.psf Parameter: 9 -> "SCRATCH/" VOPEN> Attempting to open::scratch//test2.psf:: OPNLGU> Unit 1 opened for WRITE access to scratch//test2.psf
CHARMM> write psf card unit 1 RDTITL> * AFTER QCHEM RDTITL> *
CHARMM>
CHARMM> open write card unit 1 name @9/test2.coor Parameter: 9 -> "SCRATCH/" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::scratch//test2.coor:: OPNLGU> Unit 1 opened for WRITE access to scratch//test2.coor
CHARMM> write coor card unit 1 RDTITL> * AFTER QCHEM RDTITL> * VCLOSE: Closing unit 1 with status "KEEP"
CHARMM>
CHARMM> scal xcomp = x
CHARMM> scal ycomp = y
CHARMM> scal zcomp = z
CHARMM>
CHARMM> scal x = dx
CHARMM> scal y = dy
CHARMM> scal z = dz
CHARMM>
CHARMM> open write card unit 1 name @9/test2.frc Parameter: 9 -> "SCRATCH/" VOPEN> Attempting to open::scratch//test2.frc:: OPNLGU> Unit 1 opened for WRITE access to scratch//test2.frc
CHARMM> write coor card unit 1 RDTITL> * FORCES AFTER QCHEM RDTITL> * VCLOSE: Closing unit 1 with status "KEEP"
CHARMM>
CHARMM> ! restore forces CHARMM> scal x = xcomp
CHARMM> scal y = ycomp
CHARMM> scal z = zcomp
CHARMM>
CHARMM> test first tol 0.0 step 0.0005
TESTFD: Parameters: STEP= 0.00050 MASSweighting= 0 TESTFD: The following first derivatives differ by more than TOL= 0.000000
DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 1 X ( MPEP 1 ALA N ) -2.81443309 -2.81439757 -0.00003553 1 Y ( MPEP 1 ALA N ) -3.91834116 -3.91824168 -0.00009948 1 Z ( MPEP 1 ALA N ) 0.58571141 0.58576494 -0.00005353 2 X ( MPEP 1 ALA HT1 ) -0.64367541 -0.64367478 -0.00000064 2 Y ( MPEP 1 ALA HT1 ) 0.30697142 0.30700896 -0.00003754 2 Z ( MPEP 1 ALA HT1 ) -0.52714316 -0.52714790 0.00000475 3 X ( MPEP 1 ALA HT2 ) -0.44958922 -0.44957426 -0.00001495 3 Y ( MPEP 1 ALA HT2 ) 1.37401804 1.37396043 0.00005761 3 Z ( MPEP 1 ALA HT2 ) -0.15046496 -0.15052316 0.00005820 4 X ( MPEP 1 ALA HT3 ) -0.61319587 -0.61325396 0.00005808 4 Y ( MPEP 1 ALA HT3 ) 0.45257292 0.45257002 0.00000290 4 Z ( MPEP 1 ALA HT3 ) 0.41056656 0.41058849 -0.00002193 5 X ( MPEP 1 ALA CA ) 0.02135135 0.02130904 0.00004231 5 Y ( MPEP 1 ALA CA ) -0.11917364 -0.11914072 -0.00003291 5 Z ( MPEP 1 ALA CA ) -0.75962843 -0.75961932 -0.00000911 6 X ( MPEP 1 ALA HA ) 0.55309351 0.55308605 0.00000746 6 Y ( MPEP 1 ALA HA ) 2.03572808 2.03575123 -0.00002314 6 Z ( MPEP 1 ALA HA ) -0.83902988 -0.83898984 -0.00004004 7 X ( MPEP 1 ALA CB ) -0.96195213 -0.96196191 0.00000977 7 Y ( MPEP 1 ALA CB ) -4.20652735 -4.20647510 -0.00005225 7 Z ( MPEP 1 ALA CB ) -0.50714674 -0.50716748 0.00002075 8 X ( MPEP 1 ALA HB1 ) 0.11549743 0.11548787 0.00000956 8 Y ( MPEP 1 ALA HB1 ) 0.01953902 0.01947969 0.00005933 8 Z ( MPEP 1 ALA HB1 ) -0.09949109 -0.09949198 0.00000090 9 X ( MPEP 1 ALA HB2 ) 0.20088382 0.20079761 0.00008620 9 Y ( MPEP 1 ALA HB2 ) 0.25558720 0.25565825 -0.00007105 9 Z ( MPEP 1 ALA HB2 ) -0.28475464 -0.28472659 -0.00002806 10 X ( MPEP 1 ALA HB3 ) 0.34490250 0.34491987 -0.00001737 10 Y ( MPEP 1 ALA HB3 ) 0.34330937 0.34328407 0.00002530 10 Z ( MPEP 1 ALA HB3 ) -0.14125036 -0.14131579 0.00006543 11 X ( MPEP 1 ALA C ) -55.17532441 -55.17492631 -0.00039810 11 Y ( MPEP 1 ALA C ) -152.94118555 -152.94141577 0.00023022 11 Z ( MPEP 1 ALA C ) 22.49208247 22.49208199 0.00000048 12 X ( MPEP 1 ALA OT1 ) 46.24021003 46.24035495 -0.00014491 12 Y ( MPEP 1 ALA OT1 ) -15.76477616 -15.76491895 0.00014279 12 Z ( MPEP 1 ALA OT1 ) 3.78885511 3.78885510 0.00000001 13 X ( MPEP 1 ALA OT2 ) -35.96981453 -35.97032234 0.00050781 13 Y ( MPEP 1 ALA OT2 ) 14.58042892 14.58043167 -0.00000275 13 Z ( MPEP 1 ALA OT2 ) -1.55253020 -1.55247735 -0.00005285 14 X ( MPEP 1 ALA QQH1) 49.15204719 49.15200338 0.00004381 14 Y ( MPEP 1 ALA QQH1) 157.58184856 157.58213091 -0.00028235 14 Z ( MPEP 1 ALA QQH1) -22.41577635 -22.41570612 -0.00007023
TESTFD: A total of 0 elements were within the tolerance
CHARMM>
CHARMM> stop Parallel load balance (sec.): Node Eext Eint Wait Comm List Integ Total 0 0.0 227.8 0.0 0.0 0.0 0.0 227.8
$$$$$$ New timer profile Local node$$$$$ List time 0.00032 Other: 0.00000 Electrostatic & VDW 0.00547 Other: 0.00000 Nonbond force 0.01030 Other: 0.00483 Bond energy 0.00200 Other: 0.00000 Angle energy 0.00705 Other: 0.00000 Dihedral energy 0.00605 Other: 0.00000 Restraints energy 0.00138 Other: 0.00000 INTRNL energy 227.81570 Other: 227.79923 Comm force 0.00413 Other: 0.00000 Energy time 227.83400 Other: 0.00386 Total time 227.93231 Other: 0.09799
$$$$$$ Average profile $$$$$
List time 0.00032 Other: 0.00000 Electrostatic & VDW 0.00547 Other: 0.00000 Nonbond force 0.01030 Other: 0.00483 Bond energy 0.00200 Other: 0.00000 Angle energy 0.00705 Other: 0.00000 Dihedral energy 0.00605 Other: 0.00000 Restraints energy 0.00138 Other: 0.00000 INTRNL energy 227.81570 Other: 227.79923 Comm force 0.00413 Other: 0.00000 Energy time 227.83400 Other: 0.00386 Total time 227.93231 Other: 0.09799
NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 80160 STACK CURRENTLY IN USE IS 0 NO WARNINGS WERE ISSUED HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 0 MAXIMUM SPACE USED IS 7492 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0
$$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 3.80 MINUTES CPU TIME: 0.58 SECONDS $comment qchem control file needed for the alanine_qchem.inp test case $end
$rem exchange HF basis sto-3g qm_mm true jobtype force symmetry off sym_ignore true print_input false qmmm_print true $end
$molecule -1 1 $end * Alalnine test case for QM(GAMESS)/MM * CTERM is QM and the rest is MM * Link atom is between CA and C * The final result after 10 steps of the abnr minimization is * ABNR> 10-116448.48250 13.05082 4.58542 0.01550 * stream datadir.def if ?gamess .ne. 1 then stop read rtf card * Taken from top_all22_prot.inp * 22 1 MASS 1 H 1.00800 ! polar H MASS 2 HC 1.00800 ! N-ter H MASS 3 HA 1.00800 ! nonpolar H MASS 6 HB 1.00800 ! backbone H MASS 20 C 12.01100 ! polar C MASS 22 CT1 12.01100 ! aliphatic sp3 C for CH MASS 24 CT3 12.01100 ! aliphatic sp3 C for CH3 MASS 32 CC 12.01100 ! carbonyl C for sidechains asn,asp,gln,glu MASS 54 NH1 14.00700 ! peptide nitrogen MASS 56 NH3 14.00700 ! ammonium nitrogen MASS 70 O 15.99900 ! carbonyl oxygen MASS 72 OC 15.99900 ! carboxylate oxygen mass 9 QQH 1.00800 ! link atom
DECL -CA DECL -C DECL -O DECL +N DECL +HN DECL +CA
DEFA FIRS NTER LAST CTER AUTO ANGLES DIHE
RESI ALA 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB2 ATOM CB CT3 -0.27 ! | \ ATOM HB1 HA 0.09 ! | HB3 ATOM HB2 HA 0.09 ! O=C ATOM HB3 HA 0.09 ! | GROUP ! ATOM C C 0.51 ATOM O O -0.51 BOND CB CA N HN N CA O C BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114
PRES CTER -1.00 ! standard C-terminus GROUP ! use in generate statement ATOM C CC 0.34 ! OT2 ATOM OT1 OC -0.67 ! // ATOM OT2 OC -0.67 ! -C DELETE ATOM O ! \\ BOND C OT1 C OT2 ! OT1 IMPR OT1 CA OT2 C ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
PRES NTER 1.00 ! standard N-terminus GROUP ! use in generate statement ATOM N NH3 -0.30 ! ATOM HT1 HC 0.33 ! HT1 ATOM HT2 HC 0.33 ! / ATOM HT3 HC 0.33 ! --CA--N--HT2 ATOM CA CT1 0.21 ! | \ ATOM HA HB 0.10 ! HA HT3 DELETE ATOM HN BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 end read param card * from par_all22_prot.inp *
BONDS CT1 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 HC 403.000 1.0400 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION ! adm jr. 7/23/91, acetic acid NH3 CT1 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) CT3 CT1 222.500 1.5380 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 322.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HB CT1 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) qqh cc 0.0 1.0 ! Link atom
ANGLES NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 HC 44.000 109.5000 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/09/92, for ALA cter NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HB CT1 CT3 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP ! new aliphatics, adm jr., 2/3/92 OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO ! adm jr. 7/23/91, correction, ACETATE (KK) qqh cc ct1 0.0 0.0 ! Link atom
DIHEDRALS OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO ! adm jr. 4/17/94, zwitterionic glycine X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL ! 0.715->0.10 METHYLAMMONIUM (KK) X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
IMPROPER OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION ! 90.0->96.0 acetate, single impr (KK)
NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - cutnb 13.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO ! NMA pure solvent, adm jr., 3/3/93 CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO ! adm jr. 3/3/92, acetic acid heat of solvation CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! isobutane pure solvent properties, adm jr, 2/3/92 CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC ! same as TIP3P hydrogen, adm jr., 7/20/89 HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HC 0.000000 -0.046000 0.224500 ! ALLOW POL ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) NH3 0.000000 -0.200000 1.850000 ! ALLOW POL ! adm jr. O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION ! JG 8/27/89 qqh 0.000000 0.000000 0.000000 ! Link atom end read sequ ala 1 gene mpep setup ic param ic seed mpep 1 n mpep 1 ca mpep 1 c ic build mini abnr nstep 1000 nprint 1000 addl qqh1 mpep 1 c mpep 1 ca define qm sele atom mpep 1 c .or. atom mpep 1 ot1 - .or. atom mpep 1 ot2 end
! names in quotes so they are lowercase envi input "data/ala.str" envi ericfmt "data/ericfmt.dat" envi output "scratch/ala.gms" envi punch "scratch/test.dat" envi dictnry "scratch/test.f10" envi work15 "scratch/test.f15" envi dasort "scratch/test.f20" envi dftgrid "scratch/test.f21" envi dftints "scratch/test.f22" gamess remove noguess sele qm end mini abnr nstep 10 nprint 10 test first tol 0.0 step 0.0005 stop $CONTRL COORD=UNIQUE NOSYM=1 ICHARG=-1 SCFTYP=RHF ! runtyp=prop ! nprint=-5 RUNTYP=GRADIENT ! RUNTYP=OPTIMIZE ! EXETYP=CHECK ! MOLPLT=.TRUE. $END $SYSTEM MEMORY=500000 TIMLIM=100000 $END $BASIS ! GBASIS=AM1 GBASIS=STO NGAUSS=3 ! GBASIS=N31 NGAUSS=6 ! NDFUNC=3 NPFUNC=3 ! DIFFSP=.TRUE. DIFFS=.TRUE. $END $SCF DIRSCF=.True. diis=.true. $END $STATPT NSTEP=100 OPTTOL=0.00000001 $END $DATA
$END !$ELPOT IEPOT=1 where=pdc $END 1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 33a2 February 15, 2006 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.4.20-28.9smp(i686)@n190.lobos.nih.go Created on 3/21/ 6 at 0:29: 3 by user: hlwood
Maximum number of ATOMS: 25140, and RESidues: 14000 Current HEAP size: 2048000, and STACK size: 8000000
Processing passed argument "-p4wd" RDTITL> * ALALNINE TEST CASE FOR QM(GAMESS)/MM RDTITL> * CTERM IS QM AND THE REST IS MM RDTITL> * LINK ATOM IS BETWEEN CA AND C RDTITL> * THE FINAL RESULT AFTER 10 STEPS OF THE ABNR MINIMIZATION IS RDTITL> * ABNR> 10-116448.48250 13.05082 4.58542 0.01550 RDTITL> *
CHARMM>
CHARMM> stream datadir.def VOPEN> Attempting to open::datadir.def:: OPNLGU> Unit 99 opened for READONLY access to datadir.def
INPUT STREAM SWITCHING TO UNIT 99 RDTITL> * CHARMM TESTCASE DATA DIRECTORY ASSIGNMENT RDTITL> * Parameter: IN1 <- ""
CHARMM> faster on MISCOM> FAST option: EXPANDED (limited fast routines)
CHARMM> set 0 data/ ! input data directory Parameter: 0 <- "DATA/"
CHARMM> set 9 scratch/ ! scratch directory Parameter: 9 <- "SCRATCH/"
CHARMM> return VCLOSE: Closing unit 99 with status "KEEP"
RETURNING TO INPUT STREAM 5
CHARMM>
CHARMM> if ?gamess .ne. 1 then stop RDCMND substituted energy or value "?GAMESS" to "1" Comparing "1" and "1". IF test evaluated as false. Skipping command
CHARMM>
CHARMM> read rtf card MAINIO> Residue topology file being read from unit 5. RDTITL> * TAKEN FROM TOP_ALL22_PROT.INP RDTITL> *
CHARMM>
CHARMM> read param card
PARAMETER FILE BEING READ FROM UNIT 5 RDTITL> * FROM PAR_ALL22_PROT.INP RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM>
CHARMM> read sequ ala 1
CHARMM> gene mpep setup THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE GENPSF> Segment 1 has been generated. Its identifier is MPEP. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 1 Number of atoms = 13 Number of groups = 3 Number of bonds = 12 Number of angles = 21 Number of dihedrals = 24 Number of impropers = 1 Number of cross-terms = 0 Number of HB acceptors = 2 Number of HB donors = 3 Number of NB exclusions = 0 Total charge = 0.00000
CHARMM>
CHARMM> ic param
CHARMM> ic seed mpep 1 n mpep 1 ca mpep 1 c
CHARMM> ic build ALL POSSIBLE COORDINATES HAVE BEEN PLACED
CHARMM>
CHARMM> mini abnr nstep 1000 nprint 1000
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions.
General atom nonbond list generation found: 45 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES ABNER> An energy minimization has been requested.
EIGRNG = 0.0005000 MINDIM = 5 NPRINT = 1000 NSTEP = 1000 PSTRCT = 0.0000000 SDSTP = 0.0200000 STPLIM = 1.0000000 STRICT = 0.1000000 TOLFUN = 0.0000000 TOLGRD = 0.0000000 TOLITR = 100 TOLSTP = 0.0000000 FMEM = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER ------MINI> 0 -32.94894 0.00000 8.35393 0.00000 MINI INTERN> 0.07799 0.71822 0.06446 0.02172 0.00000 MINI EXTERN> 3.07138 -36.90272 0.00000 0.00000 0.00000 ------UPDECI: Nonbond update at step 82 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 79 ATOM PAIRS AND 0 GROUP PAIRS
General atom nonbond list generation found: 45 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
MINI> 1000 -36.80908 3.86014 0.00000 0.00000 MINI INTERN> 0.48093 2.50118 0.47296 1.79235 0.01040 MINI EXTERN> 5.06122 -47.12813 0.00000 0.00000 0.00000 ------
ABNER> Minimization exiting with number of steps limit ( 1000) exceeded.
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ABNR EXTERN: VDWaals ELEC HBONds ASP USER ------ABNR> 1000 -36.80908 3.86014 0.00000 0.00000 ABNR INTERN> 0.48093 2.50118 0.47296 1.79235 0.01040 ABNR EXTERN> 5.06122 -47.12813 0.00000 0.00000 0.00000 ------
CHARMM>
CHARMM> addl qqh1 mpep 1 c mpep 1 ca
Message from MAPIC: Atom numbers are changed. ADDLNAT: Link atom placed 1.00000 A from QM atom. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 1 Number of atoms = 14 Number of groups = 4 Number of bonds = 14 Number of angles = 22 Number of dihedrals = 24 Number of impropers = 1 Number of cross-terms = 0 Number of HB acceptors = 2 Number of HB donors = 3 Number of NB exclusions = 0 Total charge = 0.00000
CHARMM>
CHARMM> define qm sele atom mpep 1 c .or. atom mpep 1 ot1 - CHARMM> .or. atom mpep 1 ot2 end SELRPN> 3 atoms have been selected out of 14
CHARMM>
CHARMM> ! names in quotes so they are lowercase CHARMM> envi input "data/ala.str"
CHARMM> envi ericfmt "data/ericfmt.dat"
CHARMM> envi output "scratch/ala.gms"
CHARMM> envi punch "scratch/test.dat"
CHARMM> envi dictnry "scratch/test.f10"
CHARMM> envi work15 "scratch/test.f15"
CHARMM> envi dasort "scratch/test.f20"
CHARMM> envi dftgrid "scratch/test.f21"
CHARMM> envi dftints "scratch/test.f22"
CHARMM>
CHARMM> gamess remove noguess sele qm end SELRPN> 3 atoms have been selected out of 14 GUKINT> REMOve: Classical energies within QM atoms are removed. GUKINT> No EXGRoup: QM/MM Elec. for link atom host only is removed. GUKINT> NOGUess: Initial guess obtained from previous step. GUKINT> No QINP: Charges will be based on atomic numbers. ------GUKINT: Classical atoms excluded from the QM calculation: 5 MPEP 1 ALA CA GUKINT: Quantum mechanical atoms: 11 MPEP 1 ALA C 12 MPEP 1 ALA OT1 13 MPEP 1 ALA OT2 GUKINT: Quantum mechanical link atoms: 14 MPEP 1 ALA QQH1 ------FINDEL: Quantum atom 11 MPEP 1 ALA C assigned to element: C 6 FINDEL: Quantum atom 12 MPEP 1 ALA OT1 assigned to element: O 8 FINDEL: Quantum atom 13 MPEP 1 ALA OT2 assigned to element: O 8 FINDEL: Quantum atom 14 MPEP 1 ALA QQH1 assigned to element: QQH 1
GAMDFN> Some atoms will be treated quantum mechanically.
The number of quantum mechanical atoms = 4 Of which the number of QM/MM link atoms = 1 The number of molecular mechanical atoms = 10 The number of MM atoms excluded from QM = 1
QM/MM repulsion (a.u.,kcal/mole) = 3.18210009 1996.79803453 QM/MM total en. (a.u.,kcal/mole) = 3.18210009 1996.79803453
CHARMM>
CHARMM> mini abnr nstep 10 nprint 10
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions.
General atom nonbond list generation found: 51 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
ABNER> An energy minimization has been requested.
EIGRNG = 0.0005000 MINDIM = 5 NPRINT = 10 NSTEP = 10 PSTRCT = 0.0000000 SDSTP = 0.0200000 STPLIM = 1.0000000 STRICT = 0.1000000 TOLFUN = 0.0000000 TOLGRD = 0.0000000 TOLITR = 100 TOLSTP = 0.0000000 FMEM = 0.0000000 EANGLFS> Warning: Angle 22 is almost linear. Derivatives may be affected for atoms: 14 11 5 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI QUANTUM: QMELec QMVDw ------MINI> 0-116435.43168 116398.62260 37.37004 0.00000 MINI INTERN> 0.40179 2.48726 0.47262 1.79235 0.00000 MINI EXTERN> 5.06122 2.30201 0.00000 0.00000 0.00000 MINI QUANTM> -116447.94894 0.00000 ------MINI> 10-116448.48250 13.05082 4.58542 0.01722 MINI INTERN> 0.31031 2.40875 0.51589 1.79419 0.00000 MINI EXTERN> 5.71162 2.33705 0.00000 0.00000 0.00000 MINI QUANTM> -116461.56031 0.00000 ------
ABNER> Minimization exiting with number of steps limit ( 10) exceeded.
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ABNR EXTERN: VDWaals ELEC HBONds ASP USER ABNR QUANTUM: QMELec QMVDw ------ABNR> 10-116448.48250 13.05082 4.58542 0.01550 ABNR INTERN> 0.31031 2.40875 0.51589 1.79419 0.00000 ABNR EXTERN> 5.71162 2.33705 0.00000 0.00000 0.00000 ABNR QUANTM> -116461.56031 0.00000 ------
CHARMM>
CHARMM> test first tol 0.0 step 0.0005 TESTFD: Parameters: STEP= 0.00050 MASSweighting= 0 TESTFD: The following first derivatives differ by more than TOL= 0.000000
DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 1 X ( MPEP 1 ALA N ) -3.35569052 -3.35559338 -0.00009715 1 Y ( MPEP 1 ALA N ) -14.70193992 -14.70182056 -0.00011936 1 Z ( MPEP 1 ALA N ) 2.86191677 2.86188732 0.00002946 2 X ( MPEP 1 ALA HT1 ) 1.51083880 1.51083065 0.00000814 2 Y ( MPEP 1 ALA HT1 ) 3.19576897 3.19571079 0.00005818 2 Z ( MPEP 1 ALA HT1 ) 2.75655665 2.75655984 -0.00000320 3 X ( MPEP 1 ALA HT2 ) -1.90594939 -1.90598569 0.00003630 3 Y ( MPEP 1 ALA HT2 ) 8.33924609 8.33928552 -0.00003943 3 Z ( MPEP 1 ALA HT2 ) -1.24177100 -1.24178456 0.00001355 4 X ( MPEP 1 ALA HT3 ) 1.72438906 1.72440801 -0.00001894 4 Y ( MPEP 1 ALA HT3 ) 2.38329931 2.38324465 0.00005467 4 Z ( MPEP 1 ALA HT3 ) -4.10362350 -4.10360820 -0.00001530 5 X ( MPEP 1 ALA CA ) -0.09037398 -0.09043221 0.00005823 5 Y ( MPEP 1 ALA CA ) -2.66020758 -2.66026030 0.00005273 5 Z ( MPEP 1 ALA CA ) -1.87621836 -1.87618039 -0.00003797 6 X ( MPEP 1 ALA HA ) 0.01442591 0.01441404 0.00001187 6 Y ( MPEP 1 ALA HA ) 0.28468331 0.28467769 0.00000562 6 Z ( MPEP 1 ALA HA ) -0.10532314 -0.10532732 0.00000418 7 X ( MPEP 1 ALA CB ) -3.47436807 -3.47436185 -0.00000622 7 Y ( MPEP 1 ALA CB ) -4.62133267 -4.62138948 0.00005682 7 Z ( MPEP 1 ALA CB ) 3.27170922 3.27168798 0.00002124 8 X ( MPEP 1 ALA HB1 ) 1.05176793 1.05170185 0.00006608 8 Y ( MPEP 1 ALA HB1 ) 3.63591320 3.63592761 -0.00001441 8 Z ( MPEP 1 ALA HB1 ) -0.46839384 -0.46838823 -0.00000561 9 X ( MPEP 1 ALA HB2 ) -0.42037541 -0.42037322 -0.00000219 9 Y ( MPEP 1 ALA HB2 ) -0.06870726 -0.06874427 0.00003701 9 Z ( MPEP 1 ALA HB2 ) -1.36606592 -1.36605023 -0.00001569 10 X ( MPEP 1 ALA HB3 ) 1.92029661 1.92028460 0.00001201 10 Y ( MPEP 1 ALA HB3 ) -0.55673867 -0.55674346 0.00000478 10 Z ( MPEP 1 ALA HB3 ) -0.35424923 -0.35426619 0.00001696 11 X ( MPEP 1 ALA C ) -0.92507337 -0.92480236 -0.00027101 11 Y ( MPEP 1 ALA C ) 10.10140684 10.10128659 0.00012024 11 Z ( MPEP 1 ALA C ) -0.55891877 -0.55904394 0.00012517 12 X ( MPEP 1 ALA OT1 ) 4.35520602 4.35562301 -0.00041699 12 Y ( MPEP 1 ALA OT1 ) -3.46065895 -3.46096561 0.00030666 12 Z ( MPEP 1 ALA OT1 ) 1.13735602 1.13723600 0.00012001 13 X ( MPEP 1 ALA OT2 ) -2.19655746 -2.19723987 0.00068241 13 Y ( MPEP 1 ALA OT2 ) 0.49215576 0.49232463 -0.00016887 13 Z ( MPEP 1 ALA OT2 ) 0.62426590 0.62429476 -0.00002885 14 X ( MPEP 1 ALA QQH1) 1.79146386 1.79157704 -0.00011318 14 Y ( MPEP 1 ALA QQH1) -2.36288844 -2.36276141 -0.00012702 14 Z ( MPEP 1 ALA QQH1) -0.57724081 -0.57684243 -0.00039838
TESTFD: A total of 0 elements were within the tolerance
CHARMM>
CHARMM>
Parallel load balance (sec.): Node Eext Eint Wait Comm List Integ Total 0 0.0 10.9 0.0 0.0 0.0 0.0 10.9 VCLOSE: Closing unit 7 with status "KEEP" VCLOSE: Closing unit 10 with status "KEEP" VCLOSE: Closing unit 80 with status "KEEP" VCLOSE: Closing unit 81 with status "KEEP"
NORMAL TERMINATION BY END OF FILE MAXIMUM STACK SPACE USED IS 17512 STACK CURRENTLY IN USE IS 0 NO WARNINGS WERE ISSUED HEAP PRINTOUT- HEAP SIZE 2048000 SPACE CURRENTLY IN USE IS 0 MAXIMUM SPACE USED IS 7840 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 2048000 NEXT: 0
$$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 11.05 SECONDS CPU TIME: 8.95 SECONDS * CHARMM / GAMESS-UK Testcase c28test/alanine_guk.inp * Author: Paul Sherwood * Alalnine test case for QM(GAMESS)/MM using GAMESS-UK interface * CTERM is QM and the rest is MM Link atom is between CA and C * Runs ~ 3 min on HP-735 * Requires alanine_guk.in * if ?gamessuk .ne. 1 then stop read rtf card * Taken from top_all22_prot.inp * 22 1 MASS 1 H 1.00800 ! polar H MASS 2 HC 1.00800 ! N-ter H MASS 3 HA 1.00800 ! nonpolar H MASS 6 HB 1.00800 ! backbone H MASS 20 C 12.01100 ! polar C MASS 22 CT1 12.01100 ! aliphatic sp3 C for CH MASS 24 CT3 12.01100 ! aliphatic sp3 C for CH3 MASS 32 CC 12.01100 ! carbonyl C for sidechains asn,asp,gln,glu MASS 54 NH1 14.00700 ! peptide nitrogen MASS 56 NH3 14.00700 ! ammonium nitrogen MASS 70 O 15.99900 ! carbonyl oxygen MASS 72 OC 15.99900 ! carboxylate oxygen mass 9 QQH 1.00800 ! link atom
DECL -CA DECL -C DECL -O DECL +N DECL +HN DECL +CA
DEFA FIRS NTER LAST CTER AUTO ANGLES DIHE
RESI ALA 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB2 ATOM CB CT3 -0.27 ! | \ ATOM HB1 HA 0.09 ! | HB3 ATOM HB2 HA 0.09 ! O=C ATOM HB3 HA 0.09 ! | GROUP ! ATOM C C 0.51 ATOM O O -0.51 BOND CB CA N HN N CA O C BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114
PRES CTER -1.00 ! standard C-terminus GROUP ! use in generate statement ATOM C CC 0.34 ! OT2 ATOM OT1 OC -0.67 ! // ATOM OT2 OC -0.67 ! -C DELETE ATOM O ! \\ BOND C OT1 C OT2 ! OT1 IMPR OT1 CA OT2 C ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
PRES NTER 1.00 ! standard N-terminus GROUP ! use in generate statement ATOM N NH3 -0.30 ! ATOM HT1 HC 0.33 ! HT1 ATOM HT2 HC 0.33 ! / ATOM HT3 HC 0.33 ! --CA--N--HT2 ATOM CA CT1 0.21 ! | \ ATOM HA HB 0.10 ! HA HT3 DELETE ATOM HN BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 end read param card * from par_all22_prot.inp *
BONDS CT1 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 HC 403.000 1.0400 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION ! adm jr. 7/23/91, acetic acid NH3 CT1 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) CT3 CT1 222.500 1.5380 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 322.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HB CT1 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) qqh cc 0.0 1.0 ! Link atom
ANGLES NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 HC 44.000 109.5000 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/09/92, for ALA cter NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HB CT1 CT3 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP ! new aliphatics, adm jr., 2/3/92 OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO ! adm jr. 7/23/91, correction, ACETATE (KK) qqh cc ct1 0.0 0.0 ! Link atom
DIHEDRALS OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO ! adm jr. 4/17/94, zwitterionic glycine X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL ! 0.715->0.10 METHYLAMMONIUM (KK) X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
IMPROPER OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION ! 90.0->96.0 acetate, single impr (KK)
NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - cutnb 13.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO ! NMA pure solvent, adm jr., 3/3/93 CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO ! adm jr. 3/3/92, acetic acid heat of solvation CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! isobutane pure solvent properties, adm jr, 2/3/92 CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC ! same as TIP3P hydrogen, adm jr., 7/20/89 HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HC 0.000000 -0.046000 0.224500 ! ALLOW POL ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) NH3 0.000000 -0.200000 1.850000 ! ALLOW POL ! adm jr. O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION ! JG 8/27/89 qqh 0.000000 0.000000 0.000000 ! Link atom end read sequ ala 1 gene mpep setup ic param ic seed mpep 1 n mpep 1 ca mpep 1 c ic build mini abnr nstep 1000 nprint 1000 addl qqh1 mpep 1 c mpep 1 ca
! Uncomment to mix GAMESS-UK and CHARMM output ! envi "gamess.out" "stdout"
! This is needed to save ED3 between steps envi "ed3" "charmm.ed3" envi "gamess.in" "data/alanine_guk.in" define qm sele atom mpep 1 c .or. atom mpep 1 ot1 - .or. atom mpep 1 ot2 end gamess remove sele qm end open write card unit 1 name test.psf write psf card unit 1 * after gamess * open write card unit 1 name test.coor write coor card unit 1 * after gamess * energy open write card unit 1 name test2.psf write psf card unit 1 * after gamess * open write card unit 1 name test2.coor write coor card unit 1 * after gamess * scal xcomp = x scal ycomp = y scal zcomp = z scal x = dx scal y = dy scal z = dz open write card unit 1 name test2.frc write coor card unit 1 * forces after gamess *
! restore forces scal x = xcomp scal y = ycomp scal z = zcomp test first tol 0.0 step 0.0005 core 5000000 chm append title qm region for charmm charge -1 adapt off nosym noprint distance analysis basis sto3g scftype rhf runtype gradient vectors atoms enter 1 1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 31a2 February 15, 2004 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.6.9-1.667smp(i686)@de9.lobos.nih.gov Created on 3/21/ 6 at 0:26: 3 by user: hlwood
Maximum number of ATOMS: 25140, and RESidues: 14000 Current HEAP size: 2048000, and STACK size: 4000000
Processing passed argument "-p4wd" RDTITL> * CHARMM / GAMESS-UK TESTCASE C28TEST/ALANINE_GUK.INP RDTITL> * AUTHOR: PAUL SHERWOOD RDTITL> * ALALNINE TEST CASE FOR QM(GAMESS)/MM USING GAMESS-UK INTERFACE RDTITL> * CTERM IS QM AND THE REST IS MM LINK ATOM IS BETWEEN CA AND C RDTITL> * RUNS ~ 3 MIN ON HP-735 RDTITL> * REQUIRES ALANINE_GUK.IN RDTITL> *
CHARMM>
CHARMM> if ?gamessuk .ne. 1 then stop RDCMND substituted energy or value "?GAMESSUK" to "1" Comparing "1" and "1". IF test evaluated as false. Skipping command
CHARMM>
CHARMM> read rtf card MAINIO> Residue topology file being read from unit 5. RDTITL> * TAKEN FROM TOP_ALL22_PROT.INP RDTITL> *
CHARMM>
CHARMM> read param card
PARAMETER FILE BEING READ FROM UNIT 5 RDTITL> * FROM PAR_ALL22_PROT.INP RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM>
CHARMM> read sequ ala 1
CHARMM> gene mpep setup THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE GENPSF> Segment 1 has been generated. Its identifier is MPEP. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 1 Number of atoms = 13 Number of groups = 3 Number of bonds = 12 Number of angles = 21 Number of dihedrals = 24 Number of impropers = 1 Number of cross-terms = 0 Number of HB acceptors = 2 Number of HB donors = 3 Number of NB exclusions = 0 Total charge = 0.00000
CHARMM>
CHARMM> ic param
CHARMM> ic seed mpep 1 n mpep 1 ca mpep 1 c
CHARMM> ic build
CHARMM>
CHARMM> mini abnr nstep 1000 nprint 1000
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions.
General atom nonbond list generation found: 45 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
ABNER> An energy minimization has been requested.
EIGRNG = 0.0005000 MINDIM = 5 NPRINT = 1000 NSTEP = 1000 PSTRCT = 0.0000000 SDSTP = 0.0200000 STPLIM = 1.0000000 STRICT = 0.1000000 TOLFUN = 0.0000000 TOLGRD = 0.0000000 TOLITR = 100 TOLSTP = 0.0000000 FMEM = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER ------MINI> 0 -32.94894 0.00000 8.35393 0.00000 MINI INTERN> 0.07799 0.71822 0.06446 0.02172 0.00000 MINI EXTERN> 3.07138 -36.90272 0.00000 0.00000 0.00000 ------UPDECI: Nonbond update at step 82 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 79 ATOM PAIRS AND 0 GROUP PAIRS
General atom nonbond list generation found: 45 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES ABNER> Minimization exiting with function tolerance ( 0.0000000) satisfied.
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ABNR EXTERN: VDWaals ELEC HBONds ASP USER ------ABNR> 505 -36.80908 3.86014 0.00000 0.00000 ABNR INTERN> 0.48093 2.50118 0.47296 1.79235 0.01040 ABNR EXTERN> 5.06122 -47.12813 0.00000 0.00000 0.00000 ------
CHARMM>
CHARMM> addl qqh1 mpep 1 c mpep 1 ca
Message from MAPIC: Atom numbers are changed. ADDLNAT: Link atom placed 1.00000 A from QM atom. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 1 Number of atoms = 14 Number of groups = 4 Number of bonds = 14 Number of angles = 22 Number of dihedrals = 24 Number of impropers = 1 Number of cross-terms = 0 Number of HB acceptors = 2 Number of HB donors = 3 Number of NB exclusions = 0 Total charge = 0.00000
CHARMM>
CHARMM> ! Uncomment to mix GAMESS-UK and CHARMM output CHARMM> ! envi "gamess.out" "stdout" CHARMM>
CHARMM> ! This is needed to save ED3 between steps CHARMM> envi "ed3" "charmm.ed3"
CHARMM> envi "gamess.in" "data/alanine_guk.in"
CHARMM>
CHARMM> define qm sele atom mpep 1 c .or. atom mpep 1 ot1 - CHARMM> .or. atom mpep 1 ot2 end SELRPN> 3 atoms have been selected out of 14
CHARMM>
CHARMM> gamess remove sele qm end SELRPN> 3 atoms have been selected out of 14 GUKINT> REMOve: Classical energies within QM atoms are removed. GUKINT> No EXGRoup: QM/MM Elec. for link atom host only is removed. GUKINT> No QINP: Charges will be based on atomic numbers. ------GUKINT: Classical atoms excluded from the QM calculation: 5 MPEP 1 ALA CA GUKINT: Quantum mechanical atoms: 11 MPEP 1 ALA C 12 MPEP 1 ALA OT1 13 MPEP 1 ALA OT2 GUKINT: Quantum mechanical link atoms: 14 MPEP 1 ALA QQH1 ------FINDEL: Quantum atom 11 MPEP 1 ALA C assigned to element: C 6 FINDEL: Quantum atom 12 MPEP 1 ALA OT1 assigned to element: O 8 FINDEL: Quantum atom 13 MPEP 1 ALA OT2 assigned to element: O 8 FINDEL: Quantum atom 14 MPEP 1 ALA QQH1 assigned to element: QQH 1
GAMDFN> Some atoms will be treated quantum mechanically.
The number of quantum mechanical atoms = 4 Of which the number of QM/MM link atoms = 1 The number of molecular mechanical atoms = 10 The number of MM atoms excluded from QM = 1
GUK> GAMESS-UK interfaced initialised GUK> Total number of centres = 13 GUK> Input total charge= -1
CHARMM>
CHARMM> open write card unit 1 name test.psf VOPEN> Attempting to open::test.psf:: OPNLGU> Unit 1 opened for WRITE access to test.psf
CHARMM> write psf card unit 1 RDTITL> * AFTER GAMESS RDTITL> *
CHARMM>
CHARMM> open write card unit 1 name test.coor OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::test.coor:: OPNLGU> Unit 1 opened for WRITE access to test.coor
CHARMM> write coor card unit 1 RDTITL> * AFTER GAMESS RDTITL> * VCLOSE: Closing unit 1 with status "KEEP"
CHARMM>
CHARMM> energy
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions.
General atom nonbond list generation found: 51 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
EANGLFS> Warning: Angle 22 is almost linear. Derivatives may be affected for atoms: 14 11 5 ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ENER QUANTUM: QMELec QMVDw ------ENER> 0-116435.43154 116398.62246 37.37034 ENER INTERN> 0.40179 2.48726 0.47262 1.79235 0.00000 ENER EXTERN> 5.06122 2.30201 0.00000 0.00000 0.00000 ENER QUANTM> -116447.94880 0.00000 ------
CHARMM>
CHARMM> open write card unit 1 name test2.psf VOPEN> Attempting to open::test2.psf:: OPNLGU> Unit 1 opened for WRITE access to test2.psf
CHARMM> write psf card unit 1 RDTITL> * AFTER GAMESS RDTITL> *
CHARMM>
CHARMM> open write card unit 1 name test2.coor OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::test2.coor:: OPNLGU> Unit 1 opened for WRITE access to test2.coor
CHARMM> write coor card unit 1 RDTITL> * AFTER GAMESS RDTITL> * VCLOSE: Closing unit 1 with status "KEEP"
CHARMM>
CHARMM> scal xcomp = x
CHARMM> scal ycomp = y
CHARMM> scal zcomp = z
CHARMM>
CHARMM> scal x = dx
CHARMM> scal y = dy
CHARMM> scal z = dz
CHARMM>
CHARMM> open write card unit 1 name test2.frc VOPEN> Attempting to open::test2.frc:: OPNLGU> Unit 1 opened for WRITE access to test2.frc
CHARMM> write coor card unit 1 RDTITL> * FORCES AFTER GAMESS RDTITL> * VCLOSE: Closing unit 1 with status "KEEP"
CHARMM>
CHARMM> ! restore forces CHARMM> scal x = xcomp
CHARMM> scal y = ycomp
CHARMM> scal z = zcomp
CHARMM>
CHARMM> test first tol 0.0 step 0.0005
TESTFD: Parameters: STEP= 0.00050 MASSweighting= 0 TESTFD: The following first derivatives differ by more than TOL= 0.000000
DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 1 X ( MPEP 1 ALA N ) -2.81444072 -2.81433783 -0.00010289 1 Y ( MPEP 1 ALA N ) -3.91834672 -3.91825449 -0.00009224 1 Z ( MPEP 1 ALA N ) 0.58565897 0.58567595 -0.00001698 2 X ( MPEP 1 ALA HT1 ) -0.64367478 -0.64370150 0.00002671 2 Y ( MPEP 1 ALA HT1 ) 0.30698039 0.30695151 0.00002888 2 Z ( MPEP 1 ALA HT1 ) -0.52713983 -0.52716165 0.00002182 3 X ( MPEP 1 ALA HT2 ) -0.44958698 -0.44959680 0.00000982 3 Y ( MPEP 1 ALA HT2 ) 1.37401978 1.37402503 -0.00000525 3 Z ( MPEP 1 ALA HT2 ) -0.15044545 -0.15045429 0.00000884 4 X ( MPEP 1 ALA HT3 ) -0.61319603 -0.61322324 0.00002721 4 Y ( MPEP 1 ALA HT3 ) 0.45256723 0.45254738 0.00001986 4 Z ( MPEP 1 ALA HT3 ) 0.41057248 0.41058684 -0.00001436 5 X ( MPEP 1 ALA CA ) 0.02135222 0.02130990 0.00004233 5 Y ( MPEP 1 ALA CA ) -0.11916399 -0.11913110 -0.00003289 5 Z ( MPEP 1 ALA CA ) -0.75962963 -0.75962053 -0.00000911 6 X ( MPEP 1 ALA HA ) 0.55309661 0.55311211 -0.00001550 6 Y ( MPEP 1 ALA HA ) 2.03573944 2.03572563 0.00001381 6 Z ( MPEP 1 ALA HA ) -0.83900204 -0.83899331 -0.00000874 7 X ( MPEP 1 ALA CB ) -0.96195788 -0.96190088 -0.00005700 7 Y ( MPEP 1 ALA CB ) -4.20651917 -4.20655162 0.00003245 7 Z ( MPEP 1 ALA CB ) -0.50720327 -0.50721045 0.00000719 8 X ( MPEP 1 ALA HB1 ) 0.11549797 0.11548240 0.00001557 8 Y ( MPEP 1 ALA HB1 ) 0.01954017 0.01953456 0.00000560 8 Z ( MPEP 1 ALA HB1 ) -0.09949083 -0.09948431 -0.00000651 9 X ( MPEP 1 ALA HB2 ) 0.20088305 0.20086567 0.00001737 9 Y ( MPEP 1 ALA HB2 ) 0.25559112 0.25560692 -0.00001580 9 Z ( MPEP 1 ALA HB2 ) -0.28475062 -0.28476078 0.00001016 10 X ( MPEP 1 ALA HB3 ) 0.34490290 0.34490415 -0.00000125 10 Y ( MPEP 1 ALA HB3 ) 0.34331161 0.34331471 -0.00000309 10 Z ( MPEP 1 ALA HB3 ) -0.14124635 -0.14124795 0.00000159 11 X ( MPEP 1 ALA C ) -55.17546945 -55.17530460 -0.00016485 11 Y ( MPEP 1 ALA C ) -152.94127357 -152.94174541 0.00047184 11 Z ( MPEP 1 ALA C ) 22.48999294 22.49002003 -0.00002709 12 X ( MPEP 1 ALA OT1 ) 46.24363977 46.24221758 0.00142220 12 Y ( MPEP 1 ALA OT1 ) -15.76657062 -15.76559059 -0.00098002 12 Z ( MPEP 1 ALA OT1 ) 3.78888670 3.78870922 0.00017748 13 X ( MPEP 1 ALA OT2 ) -35.97347346 -35.97198756 -0.00148590 13 Y ( MPEP 1 ALA OT2 ) 14.58104721 14.58117690 -0.00012970 13 Z ( MPEP 1 ALA OT2 ) -1.55245956 -1.55244673 -0.00001283 14 X ( MPEP 1 ALA QQH1) 49.15242677 49.15216171 0.00026506 14 Y ( MPEP 1 ALA QQH1) 157.58307712 157.58236332 0.00071380 14 Z ( MPEP 1 ALA QQH1) -22.41374351 -22.41361962 -0.00012389
TESTFD: A total of 0 elements were within the tolerance
Parallel load balance (sec.): Node Eext Eint Wait Comm List Integ Total 0 0.0 29.7 0.0 0.0 0.0 0.0 29.7
$$$$$$ New timer profile Local node$$$$$
Nonbond force 0.03039 Other: 0.00000 Bond energy 0.00646 Other: 0.00000 Angle energy 0.01317 Other: 0.00000 Dihedral energy 0.02503 Other: 0.00000 Restraints energy 0.00992 Other: 0.00000 INTRNL energy 29.66890 Other: 29.61432 Comm force 0.02726 Other: 0.00000 Energy time 29.74507 Other: 0.01852 Total time 30.31829 Other: 0.57322
$$$$$$ Average profile $$$$$
Nonbond force 0.03039 Other: 0.00000 Bond energy 0.00646 Other: 0.00000 Angle energy 0.01317 Other: 0.00000 Dihedral energy 0.02503 Other: 0.00000 Restraints energy 0.00992 Other: 0.00000 INTRNL energy 29.66890 Other: 29.61432 Comm force 0.02726 Other: 0.00000 Energy time 29.74507 Other: 0.01852 Total time 30.31829 Other: 0.57322
NORMAL TERMINATION BY END OF FILE MAXIMUM STACK SPACE USED IS 47512 STACK CURRENTLY IN USE IS 0 NO WARNINGS WERE ISSUED HEAP PRINTOUT- HEAP SIZE 2048000 SPACE CURRENTLY IN USE IS 134 MAXIMUM SPACE USED IS 7598 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 2043722 NEXT: 2043825 PRINHP> ADDRESS: 2043825 LENGTH: 3644 NEXT: 2047473 PRINHP> ADDRESS: 2047473 LENGTH: 500 NEXT: 0
$$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 30.32 SECONDS CPU TIME: 26.26 SECONDS * CHARMM / GAMESS-UK Testcase c29test/alanine_scc.inp * Author: Qiang Cui (Based on the example by Paul Sherwood) * Alalnine test case for QM(SCC-DFTB)/MM using SCC-DFTB interface * CTERM is SCC-DFTB and the rest is MM Link atom is between CA and C * Requires: sccdftb.dat (contact Marcus Elstner for necessary files) * if ?sccdftb .ne. 1 then echo "Test NOT performed." stop endif read rtf card * Taken from top_all22_prot.inp * 22 1 MASS 1 H 1.00800 ! polar H MASS 2 HC 1.00800 ! N-ter H MASS 3 HA 1.00800 ! nonpolar H MASS 6 HB 1.00800 ! backbone H MASS 20 C 12.01100 ! polar C MASS 22 CT1 12.01100 ! aliphatic sp3 C for CH MASS 24 CT3 12.01100 ! aliphatic sp3 C for CH3 MASS 32 CC 12.01100 ! carbonyl C for sidechains asn,asp,gln,glu MASS 54 NH1 14.00700 ! peptide nitrogen MASS 56 NH3 14.00700 ! ammonium nitrogen MASS 70 O 15.99900 ! carbonyl oxygen MASS 72 OC 15.99900 ! carboxylate oxygen mass 9 QQH 1.00800 ! link atom
DECL -CA DECL -C DECL -O DECL +N DECL +HN DECL +CA
DEFA FIRS NTER LAST CTER AUTO ANGLES DIHE
RESI ALA 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB2 ATOM CB CT3 -0.27 ! | \ ATOM HB1 HA 0.09 ! | HB3 ATOM HB2 HA 0.09 ! O=C ATOM HB3 HA 0.09 ! | GROUP ! ATOM C C 0.51 ATOM O O -0.51 BOND CB CA N HN N CA O C BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114
PRES CTER -1.00 ! standard C-terminus GROUP ! use in generate statement ATOM C CC 0.34 ! OT2 ATOM OT1 OC -0.67 ! // ATOM OT2 OC -0.67 ! -C DELETE ATOM O ! \\ BOND C OT1 C OT2 ! OT1 IMPR OT1 CA OT2 C ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
PRES NTER 1.00 ! standard N-terminus GROUP ! use in generate statement ATOM N NH3 -0.30 ! ATOM HT1 HC 0.33 ! HT1 ATOM HT2 HC 0.33 ! / ATOM HT3 HC 0.33 ! --CA--N--HT2 ATOM CA CT1 0.21 ! | \ ATOM HA HB 0.10 ! HA HT3 DELETE ATOM HN BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 end read param card * from par_all22_prot.inp *
BONDS CT1 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 HC 403.000 1.0400 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION ! adm jr. 7/23/91, acetic acid NH3 CT1 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) CT3 CT1 222.500 1.5380 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 322.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HB CT1 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) qqh cc 0.0 1.0 ! Link atom
ANGLES NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 HC 44.000 109.5000 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/09/92, for ALA cter NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HB CT1 CT3 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP ! new aliphatics, adm jr., 2/3/92 OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO ! adm jr. 7/23/91, correction, ACETATE (KK) qqh cc ct1 0.0 0.0 ! Link atom
DIHEDRALS OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO ! adm jr. 4/17/94, zwitterionic glycine X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL ! 0.715->0.10 METHYLAMMONIUM (KK) X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
IMPROPER OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION ! 90.0->96.0 acetate, single impr (KK)
NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - cutnb 13.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO ! NMA pure solvent, adm jr., 3/3/93 CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO ! adm jr. 3/3/92, acetic acid heat of solvation CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! isobutane pure solvent properties, adm jr, 2/3/92 CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC ! same as TIP3P hydrogen, adm jr., 7/20/89 HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HC 0.000000 -0.046000 0.224500 ! ALLOW POL ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) NH3 0.000000 -0.200000 1.850000 ! ALLOW POL ! adm jr. O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION ! JG 8/27/89 qqh 0.000000 0.000000 0.000000 ! Link atom end read sequ ala 1 gene mpep setup ic param ic seed mpep 1 n mpep 1 ca mpep 1 c ic build mini abnr nstep 1000 nprint 1000 addl qqh1 mpep 1 c mpep 1 ca
! ...... Need to specify qq ...... define qm sele atom mpep 1 c .or. atom mpep 1 ot1 - .or. atom mpep 1 ot2 .or. type qq* end
! ------! ! Use the following to assign atom types (only need to do once ! WMAIN will become available after the sccdftb command) ! The sequence (O:1, N:2, C:3, H:4 has to be consistent with the ! sccdftb.dat file) scalar WMAIN set 1.0 sele qm .and. type O* SHOW end scalar WMAIN set 2.0 sele qm .and. type N* SHOW end scalar WMAIN set 3.0 sele qm .and. type C* SHOW end scalar WMAIN set 4.0 sele qm .and. type H* SHOW end ! Donot forget about the link atom scalar WMAIN set 4.0 sele qm .and. type QQ* SHOW end
! Default SCF convergence is 1.d-7, which is fine. ! 1.d-6 would give not so accurate forces sccdftb remove chrg -1 sele qm end SCFT 0.00000001 ! ! ------energy scal xcomp = x scal ycomp = y scal zcomp = z scal x = dx scal y = dy scal z = dz
! restore forces scal x = xcomp scal y = ycomp scal z = zcomp
! Check force with finite difference test first tol 0.0 step 0.0005
STOP 'SLKO_NEW/oo.spl' 'SLKO_NEW/on.spl' 'SLKO_NEW/oc.spl' 'SLKO_NEW/oh.spl' 'SLKO_NEW/no.spl' 'SLKO_NEW/nn.spl' 'SLKO_NEW/nc.spl' 'SLKO_NEW/nh.spl' 'SLKO_NEW/co.spl' 'SLKO_NEW/cn.spl' 'SLKO_NEW/cc.spl' 'SLKO_NEW/ch.spl' 'SLKO_NEW/hh.spl' 0 process started 1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 32a2 February 15, 2005 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.6.9-1.667smp(i686)@de9.lobos.nih.gov Created on 3/21/ 6 at 0:24: 0 by user: hlwood
Maximum number of ATOMS: 60120, and RESidues: 15030 Current HEAP size: 10240000, and STACK size: 2000000
Processing passed argument "-p4wd" RDTITL> * CHARMM / GAMESS-UK TESTCASE C29TEST/ALANINE_SCC.INP RDTITL> * AUTHOR: QIANG CUI (BASED ON THE EXAMPLE BY PAUL SHERWOOD) RDTITL> * ALALNINE TEST CASE FOR QM(SCC-DFTB)/MM USING SCC-DFTB INTERFACE RDTITL> * CTERM IS SCC-DFTB AND THE REST IS MM LINK ATOM IS BETWEEN CA AND C RDTITL> * REQUIRES: SCCDFTB.DAT (CONTACT MARCUS ELSTNER FOR NECESSARY FILES) RDTITL> *
CHARMM>
CHARMM> if ?sccdftb .ne. 1 then RDCMND substituted energy or value "?SCCDFTB" to "1" Comparing "1" and "1". IF test evaluated as false. Skip to ELSE or ENDIF
CHARMM>
CHARMM> read rtf card MAINIO> Residue topology file being read from unit 5. RDTITL> * TAKEN FROM TOP_ALL22_PROT.INP RDTITL> *
CHARMM>
CHARMM> read param card
PARAMETER FILE BEING READ FROM UNIT 5 RDTITL> * FROM PAR_ALL22_PROT.INP RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM>
CHARMM> read sequ ala 1
CHARMM> gene mpep setup THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE GENPSF> Segment 1 has been generated. Its identifier is MPEP. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 1 Number of atoms = 13 Number of groups = 3 Number of bonds = 12 Number of angles = 21 Number of dihedrals = 24 Number of impropers = 1 Number of cross-terms = 0 Number of HB acceptors = 2 Number of HB donors = 3 Number of NB exclusions = 0 Total charge = 0.00000
CHARMM>
CHARMM> ic param
CHARMM> ic seed mpep 1 n mpep 1 ca mpep 1 c
CHARMM> ic build
CHARMM>
CHARMM> mini abnr nstep 1000 nprint 1000
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions.
General atom nonbond list generation found: 45 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
ABNER> An energy minimization has been requested.
EIGRNG = 0.0005000 MINDIM = 5 NPRINT = 1000 NSTEP = 1000 PSTRCT = 0.0000000 SDSTP = 0.0200000 STPLIM = 1.0000000 STRICT = 0.1000000 TOLFUN = 0.0000000 TOLGRD = 0.0000000 TOLITR = 100 TOLSTP = 0.0000000 FMEM = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER ------MINI> 0 -32.94894 0.00000 8.35393 0.00000 MINI INTERN> 0.07799 0.71822 0.06446 0.02172 0.00000 MINI EXTERN> 3.07138 -36.90272 0.00000 0.00000 0.00000 ------UPDECI: Nonbond update at step 82 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 79 ATOM PAIRS AND 0 GROUP PAIRS
General atom nonbond list generation found: 45 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES ABNER> Minimization exiting with function tolerance ( 0.0000000) satisfied.
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ABNR EXTERN: VDWaals ELEC HBONds ASP USER ------ABNR> 505 -36.80908 3.86014 0.00000 0.00000 ABNR INTERN> 0.48093 2.50118 0.47296 1.79235 0.01040 ABNR EXTERN> 5.06122 -47.12813 0.00000 0.00000 0.00000 ------
CHARMM>
CHARMM> addl qqh1 mpep 1 c mpep 1 ca
Message from MAPIC: Atom numbers are changed. ADDLNAT: Link atom placed 1.00000 A from QM atom. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 1 Number of atoms = 14 Number of groups = 4 Number of bonds = 14 Number of angles = 22 Number of dihedrals = 24 Number of impropers = 1 Number of cross-terms = 0 Number of HB acceptors = 2 Number of HB donors = 3 Number of NB exclusions = 0 Total charge = 0.00000
CHARMM>
CHARMM> ! ...... Need to specify qq ...... CHARMM> define qm sele atom mpep 1 c .or. atom mpep 1 ot1 - CHARMM> .or. atom mpep 1 ot2 .or. type qq* end SELRPN> 4 atoms have been selected out of 14
CHARMM>
CHARMM> ! ------CHARMM> ! CHARMM> ! Use the following to assign atom types (only need to do once CHARMM> ! WMAIN will become available after the sccdftb command) CHARMM> ! The sequence (O:1, N:2, C:3, H:4 has to be consistent with the CHARMM> ! sccdftb.dat file) CHARMM> scalar WMAIN set 1.0 sele qm .and. type O* SHOW end The following atoms are currently set: SEGId RESId RESName .. TYPEs .. MPEP 1 ALA OT1 OT2 SELRPN> 2 atoms have been selected out of 14
CHARMM> scalar WMAIN set 2.0 sele qm .and. type N* SHOW end The following atoms are currently set: SEGId RESId RESName .. TYPEs .. SELRPN> 0 atoms have been selected out of 14
CHARMM> scalar WMAIN set 3.0 sele qm .and. type C* SHOW end The following atoms are currently set: SEGId RESId RESName .. TYPEs .. MPEP 1 ALA C SELRPN> 1 atoms have been selected out of 14
CHARMM> scalar WMAIN set 4.0 sele qm .and. type H* SHOW end The following atoms are currently set: SEGId RESId RESName .. TYPEs .. SELRPN> 0 atoms have been selected out of 14
CHARMM> ! Donot forget about the link atom CHARMM> scalar WMAIN set 4.0 sele qm .and. type QQ* SHOW end The following atoms are currently set: SEGId RESId RESName .. TYPEs .. MPEP 1 ALA QQH1 SELRPN> 1 atoms have been selected out of 14
CHARMM>
CHARMM> ! Default SCF convergence is 1.d-7, which is fine. CHARMM> ! 1.d-6 would give not so accurate forces CHARMM> sccdftb remove chrg -1 sele qm end SCFT 0.00000001 SELRPN> 4 atoms have been selected out of 14 SCCINT> REMOve: Classical energies within QM atoms are removed. SCCINT> No EXGRoup: QM/MM Elec. for link atom host only is removed. SCCINT> No QINP: Charges will be based on atomic numbers. SCCINT> DO NOT USE CUT-OFF FOR QM/MM ------SCCINT: Classical atoms excluded from the QM calculation: 5 MPEP 1 ALA CA SCCINT: Quantum mechanical atoms: 11 MPEP 1 ALA C 12 MPEP 1 ALA OT1 13 MPEP 1 ALA OT2 SCCINT: Quantum mechanical link atoms: 14 MPEP 1 ALA QQH1 SCCINT: Quantum mechanical GHO boundary atoms: NONE. ------FINDEL: Quantum atom 11 MPEP 1 ALA C assigned to element: C 6 FINDEL: Quantum atom 12 MPEP 1 ALA OT1 assigned to element: O 8 FINDEL: Quantum atom 13 MPEP 1 ALA OT2 assigned to element: O 8 FINDEL: Quantum atom 14 MPEP 1 ALA QQH1 assigned to element: QQH 1
SCCDFN> Some atoms will be treated quantum mechanically.
The number of SCCDFTB QM atoms = 4 The number of molecular mechanical atoms = 10 The number of MM atoms excluded from QM = 1 Of which the number of QM/MM link atoms = 1
CHARGE OF SCCDFTB ATOMS: -1 ** dftb (version 26.11.1998) ** enter mode, fmax, scf, scftol, read charge,dispers,EXT skip struc. file,atoms from charmm: 4 9 enter filename for output structure enter file name for sk-data of pair 1 1 skfile for pair 1 1 : /v/estor1/home/hlwood/slko/oo.spl enter file name for sk-data of pair 1 2 skfile for pair 1 2 : /v/estor1/home/hlwood/slko/on.spl enter file name for sk-data of pair 1 3 skfile for pair 1 3 : /v/estor1/home/hlwood/slko/oc.spl enter file name for sk-data of pair 1 4 skfile for pair 1 4 : /v/estor1/home/hlwood/slko/oh.spl enter file name for sk-data of pair 2 1 skfile for pair 2 1 : /v/estor1/home/hlwood/slko/no.spl enter file name for sk-data of pair 2 2 skfile for pair 2 2 : /v/estor1/home/hlwood/slko/nn.spl enter file name for sk-data of pair 2 3 skfile for pair 2 3 : /v/estor1/home/hlwood/slko/nc.spl enter file name for sk-data of pair 2 4 skfile for pair 2 4 : /v/estor1/home/hlwood/slko/nh.spl enter file name for sk-data of pair 3 1 skfile for pair 3 1 : /v/estor1/home/hlwood/slko/co.spl enter file name for sk-data of pair 3 2 skfile for pair 3 2 : /v/estor1/home/hlwood/slko/cn.spl enter file name for sk-data of pair 3 3 skfile for pair 3 3 : /v/estor1/home/hlwood/slko/cc.spl enter file name for sk-data of pair 3 4 skfile for pair 3 4 : /v/estor1/home/hlwood/slko/ch.spl enter file name for sk-data of pair 4 1 skfile for pair 4 1 : /v/estor1/home/hlwood/slko/ho.spl enter file name for sk-data of pair 4 2 skfile for pair 4 2 : /v/estor1/home/hlwood/slko/hn.spl enter file name for sk-data of pair 4 3 skfile for pair 4 3 : /v/estor1/home/hlwood/slko/hc.spl enter file name for sk-data of pair 4 4 skfile for pair 4 4 : /v/estor1/home/hlwood/slko/hh.spl Total charge of SCCDFTB molecule: -1 Total number of electrons: 18.
CHARMM> ! CHARMM> ! ------CHARMM>
CHARMM> energy
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions.
General atom nonbond list generation found: 51 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
EANGLFS> Warning: Angle 22 is almost linear. Derivatives may be affected for atoms: 14 11 5 ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ENER QUANTUM: QMELec QMVDw ------ENER> 0 -5552.00919 5515.20011 34.66035 ENER INTERN> 0.40179 2.48726 0.47262 1.79235 0.00000 ENER EXTERN> 5.06122 2.30201 0.00000 0.00000 0.00000 ENER QUANTM> -5564.52644 0.00000 ------
CHARMM>
CHARMM> scal xcomp = x
CHARMM> scal ycomp = y
CHARMM> scal zcomp = z
CHARMM>
CHARMM> scal x = dx
CHARMM> scal y = dy
CHARMM> scal z = dz
CHARMM>
CHARMM> ! restore forces CHARMM> scal x = xcomp
CHARMM> scal y = ycomp
CHARMM> scal z = zcomp
CHARMM>
CHARMM> ! Check force with finite difference CHARMM> test first tol 0.0 step 0.0005 TESTFD: Parameters: STEP= 0.00050 MASSweighting= 0 TESTFD: The following first derivatives differ by more than TOL= 0.000000
DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 1 X ( MPEP 1 ALA N ) -4.24793876 -4.24783728 -0.00010148 1 Y ( MPEP 1 ALA N ) -4.10979480 -4.10969241 -0.00010239 1 Z ( MPEP 1 ALA N ) 0.61229011 0.62701030 -0.01472018 2 X ( MPEP 1 ALA HT1 ) 0.22993604 0.22990924 0.00002680 2 Y ( MPEP 1 ALA HT1 ) 0.49889163 0.49884959 0.00004203 2 Z ( MPEP 1 ALA HT1 ) -0.19758385 -0.19760059 0.00001675 3 X ( MPEP 1 ALA HT2 ) -0.00688232 -0.00689322 0.00001090 3 Y ( MPEP 1 ALA HT2 ) -0.06771015 -0.06770522 -0.00000493 3 Z ( MPEP 1 ALA HT2 ) 0.04656835 0.04655078 0.00001757 4 X ( MPEP 1 ALA HT3 ) 0.24960627 0.24957893 0.00002734 4 Y ( MPEP 1 ALA HT3 ) 0.54320389 0.54317093 0.00003296 4 Z ( MPEP 1 ALA HT3 ) 0.04957778 0.04959233 -0.00001455 5 X ( MPEP 1 ALA CA ) 0.02135222 0.02130990 0.00004233 5 Y ( MPEP 1 ALA CA ) -0.11916399 -0.11913107 -0.00003292 5 Z ( MPEP 1 ALA CA ) -0.75962963 -0.75962053 -0.00000910 6 X ( MPEP 1 ALA HA ) 0.63314902 0.63316469 -0.00001567 6 Y ( MPEP 1 ALA HA ) 2.23510927 2.23509699 0.00001228 6 Z ( MPEP 1 ALA HA ) -0.79155815 -0.79154973 -0.00000842 7 X ( MPEP 1 ALA CB ) -0.76794569 -0.76788889 -0.00005680 7 Y ( MPEP 1 ALA CB ) -5.28557842 -5.28560305 0.00002463 7 Z ( MPEP 1 ALA CB ) -1.26329788 -1.26330195 0.00000407 8 X ( MPEP 1 ALA HB1 ) 0.12085957 0.11604726 0.00481231 8 Y ( MPEP 1 ALA HB1 ) 0.20189482 0.20188934 0.00000549 8 Z ( MPEP 1 ALA HB1 ) -0.02148006 -0.02248389 0.00100383 9 X ( MPEP 1 ALA HB2 ) 0.20495431 0.20518466 -0.00023035 9 Y ( MPEP 1 ALA HB2 ) 0.33202755 0.33204357 -0.00001602 9 Z ( MPEP 1 ALA HB2 ) 0.04039461 0.04038429 0.00001033 10 X ( MPEP 1 ALA HB3 ) 0.13071668 0.12987344 0.00084325 10 Y ( MPEP 1 ALA HB3 ) 0.47864252 0.47864452 -0.00000200 10 Z ( MPEP 1 ALA HB3 ) 0.04466387 0.04466289 0.00000097 11 X ( MPEP 1 ALA C ) -70.28697217 -70.23485093 -0.05212124 11 Y ( MPEP 1 ALA C ) -116.41586447 -116.42310171 0.00723724 11 Z ( MPEP 1 ALA C ) 21.06616592 21.06907967 -0.00291375 12 X ( MPEP 1 ALA OT1 ) 52.85247011 52.84254344 0.00992667 12 Y ( MPEP 1 ALA OT1 ) -33.17091885 -33.14782855 -0.02309030 12 Z ( MPEP 1 ALA OT1 ) 5.21710111 5.22003631 -0.00293519 13 X ( MPEP 1 ALA OT2 ) -30.12156569 -30.16019519 0.03862950 13 Y ( MPEP 1 ALA OT2 ) 1.67330498 1.67072625 0.00257874 13 Z ( MPEP 1 ALA OT2 ) -0.74270552 -0.74298111 0.00027559 14 X ( MPEP 1 ALA QQH1) 50.98826040 50.98464974 0.00361066 14 Y ( MPEP 1 ALA QQH1) 153.20595601 153.20620278 -0.00024677 14 Z ( MPEP 1 ALA QQH1) -23.30050668 -23.29946640 -0.00104028
TESTFD: A total of 0 elements were within the tolerance
CHARMM>
CHARMM> STOP Parallel load balance (sec.): Node Eext Eint Wait Comm List Integ Total 0 0.0 1.5 0.0 0.0 0.0 0.0 1.6 VCLOSE: Closing unit 71 with status "KEEP"
$$$$$$ New timer profile Local node$$$$$ Electrostatic & VDW 0.00945 Other: 0.00000 Nonbond force 0.03541 Other: 0.02596 Bond energy 0.00629 Other: 0.00000 Angle energy 0.01217 Other: 0.00000 Dihedral energy 0.01529 Other: 0.00000 Restraints energy 0.00991 Other: 0.00000 INTRNL energy 1.50995 Other: 1.46630 Comm force 0.03158 Other: 0.00000 Energy time 1.59890 Other: 0.02196 Total time 1.80660 Other: 0.20770
$$$$$$ Average profile $$$$$
Electrostatic & VDW 0.00945 Other: 0.00000 Nonbond force 0.03541 Other: 0.02596 Bond energy 0.00629 Other: 0.00000 Angle energy 0.01217 Other: 0.00000 Dihedral energy 0.01529 Other: 0.00000 Restraints energy 0.00991 Other: 0.00000 INTRNL energy 1.50995 Other: 1.46630 Comm force 0.03158 Other: 0.00000 Energy time 1.59890 Other: 0.02196 Total time 1.80660 Other: 0.20770
NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 47512 STACK CURRENTLY IN USE IS 0 NO WARNINGS WERE ISSUED HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 0 MAXIMUM SPACE USED IS 7492 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0
$$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 1.81 SECONDS CPU TIME: 0.76 SECONDS * ethanol(CH3CH2OH) qm/mm calculations * bomb -2 open unit 1 read card name etoh_top.inp read rtf card unit 1 close unit 1 open unit 1 read card name par_all22_prot_qmmm.inp read param card unit 1 close unit 1 auto angle dihe read sequ etoh 1 generate etoh setup print psf read coor card * ethanol, coordinates from HF/6-31G, initially from * pethanol_quanta_321g_2.com * total energy=- au = - kcal/mol * 09 1 1 etoh C1 0.00000 -0.40275 -1.17273 etoh 1 .0 2 1 etoh C2 0.00000 -0.45120 0.33993 etoh 1 .0 3 1 etoh O3 0.00000 0.90570 0.80935 etoh 1 .0 4 1 etoh H4 0.00000 -1.40389 -1.59009 etoh 1 .0 5 1 etoh H5 0.87639 0.12252 -1.52886 etoh 1 .0 6 1 etoh H6 -0.87639 0.12252 -1.52886 etoh 1 .0 7 1 etoh H7 0.87812 -0.97251 0.70658 etoh 1 .0 8 1 etoh H8 -0.87812 -0.97251 0.70658 etoh 1 .0 9 1 etoh H9 0.00000 0.98197 1.75667 etoh 1 .0
!ic param ic build print psf
! add the link atoms by patching
PATCH DLA etoh 1 setup test psf print psf
!PLACE THE QM LINK ATOM set dist 1.111
! coopying coor of C2 to QQL coor dupl sele bynu 8 end sele bynu 9 end !axis between C2 and C1 coor axis sele bynu 8 end sele bynu 4 end !translating QQL by 'DIST' A coor trans sele bynu 9 end axis dist @dist !PLACE THE MM LINK ATOM
! coopying coor of C1 to MML coor dupl sele bynu 4 end sele bynu 5 end !axis between C1 and C2 coor axis sele bynu 4 end sele bynu 8 end !translating MML by 'DIST' A coor trans sele bynu 5 end axis dist @dist
!select the QM region define qm sele atom etoh 1 c2 .or. atom etoh 1 o3 - .or. atom etoh 1 h7 .or. atom etoh 1 h8 - .or. atom etoh 1 h9 .or. atom etoh 1 qql show end
!select the MM region scalar wmain set @1 sele .not. qm end scalar wmain show
!open write unit 1 card name etoh.double !write coor card unit 1 open write unit 1 card name etoh.pdb coor write pdb unit 1
!anal on !anal term all gamess remove blur sele qm end energy *>> All-hydrogen topology for small model compounds used in the << *>> development of the CHARMM22 protein all-hydrogen parameters << *>>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< *>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<< *>>>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<< * 22 1 ! references ! !PROTEINS ! !MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; !Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; !Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, !C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, !W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom !empirical potential for molecular modeling and dynamics Studies of !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616.
MASS 1 H 1.00800 H ! polar H MASS 2 HC 1.00800 H ! N-ter H MASS 3 HA 1.00800 H ! nonpolar H MASS 4 QQH 1.00800 H ! FOR TIPS3P WATER HYDROGEN, QM/MM link MASS 5 HP 1.00800 H ! aromatic H MASS 6 HB 1.00800 H ! backbone H MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2 MASS 8 HR2 1.00800 H ! (+) his HE1 MASS 9 HR3 1.00800 H ! neutral his HG, HD2 MASS 10 HS 1.00800 H ! thiol hydrogen MASS 11 HA1 1.00800 H ! for alkene; RHC=CR MASS 12 HA2 1.00800 H ! for alkene; H2C=CR MASS 20 C 12.01100 C ! polar C MASS 21 CA 12.01100 C ! aromatic C MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2 MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3 MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons MASS 26 CPH2 12.01100 C ! his CE1 carbon MASS 27 CPT 12.01100 C ! trp C between rings MASS 28 CY 12.01100 C ! TRP C in pyrrole ring MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA) MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG) MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD) MASS 32 CC 12.01100 C ! carbonyl C for sidechains asn,asp,gln,glu MASS 33 CD 12.01100 C ! carbonyl C for none amides, asp,glu,cter MASS 34 CPA 12.01100 C ! heme alpha-C MASS 35 CPB 12.01100 C ! heme beta-C MASS 36 CPM 12.01100 C ! heme meso-C MASS 37 CM 12.01100 C ! heme CO carbon MASS 38 CS 12.01100 C ! thiolate carbon MASS 39 CE1 12.01100 C ! for alkene; RHC=CR MASS 40 CE2 12.01100 C ! for alkene; H2C=CR MASS 50 N 14.00700 N ! proline N MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen MASS 53 NR3 14.00700 N ! charged his ring nitrogen MASS 54 NH1 14.00700 N ! peptide nitrogen MASS 55 NH2 14.00700 N ! amide nitrogen MASS 56 NH3 14.00700 N ! ammonium nitrogen MASS 57 NC2 14.00700 N ! guanidinium nitroogen MASS 58 NY 14.00700 N ! TRP N in pyrrole ring MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal) MASS 60 NPH 14.00700 N ! heme pyrrole N MASS 70 O 15.99900 O ! carbonyl oxygen MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid MASS 72 OC 15.99900 O ! carboxylate oxygen MASS 73 OH1 15.99900 O ! hydroxyl oxygen MASS 74 OS 15.99940 O ! ester oxygen MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN MASS 76 OM 15.99900 O ! heme CO/O2 oxygen MASS 81 S 32.06000 S ! sulphur MASS 82 SM 32.06000 S ! sulfur C-S-S-C type MASS 83 SS 32.06000 S ! thiolate sulfur MASS 85 HE 4.00260 HE ! helium MASS 86 NE 20.17970 NE ! neon MASS 90 CAL 40.08000 CA ! calcium 2+ MASS 91 ZN 65.37000 ZN ! zinc (II) cation MASS 92 FE 55.84700 FE ! heme iron 56 MASS 99 DUM 0.00000 H ! dummy atom
DEFA FIRS NONE LAST NONE AUTO ANGLES DIHE
RESI etoh 0.00 ! ethanol, debdas GROUP Atom h4 ha 0.09 ! H7 H4 H5 Atom h5 ha 0.09 ! \ \ / Atom h6 ha 0.09 ! H8-C2---C1---H6 Atom c1 ct3 -0.27 ! / GROUP ! O3 Atom h7 ha 0.00 ! \ Atom h8 ha 0.00 ! H9 Atom c2 ct2 0.00 Atom o3 oh1 0.00 Atom h9 h 0.00 Bond c1 c2 Bond c1 h4 bond c1 h5 bond c1 h6 bond c2 h7 bond c2 h8 bond c2 o3 bond o3 h9 IC H4 C1 C2 O3 1.09 110.70 180.00 110.50 1.40 IC H5 C1 C2 O3 1.09 110.70 60.52 110.50 1.40 IC H6 C1 C2 O3 1.09 110.70 -60.52 110.50 1.40 IC H4 C1 C2 H7 1.09 110.70 60.40 110.70 1.09 IC H4 C1 C2 H8 1.09 110.70 -60.40 110.70 1.09 IC C1 C2 O3 H9 1.53 110.50 180.00 106.70 0.95 IC H7 C2 O3 H9 1.09 108.00 -58.79 106.70 0.95 IC H8 C2 O3 H9 1.09 108.00 58.79 106.70 0.95 patch first none last none RESI peto 1.00 ! protonated ethanol, debdas GROUP Atom h4 ha 0.09 ! H7 H4 H5 Atom h5 ha 0.09 ! \ \ / Atom h6 ha 0.09 ! H8-C2---C1---H6 Atom c1 ct3 -0.27 ! / GROUP ! O3--H10 Atom h7 ha 0.25 ! \ Atom h8 ha 0.25 ! H9 Atom c2 ct2 0.50 Atom o3 oh1 0.00 Atom h9 h 0.00 Atom h10 h 0.00 Bond c1 c2 Bond c1 h4 bond c1 h5 bond c1 h6 bond c2 h7 bond c2 h8 bond c2 o3 bond o3 h9 bond o3 h10 IC H4 C1 C2 O3 1.09 110.70 180.00 109.50 1.50 IC H5 C1 C2 O3 1.09 110.70 60.52 109.50 1.50 IC H6 C1 C2 O3 1.09 110.70 -60.52 109.50 1.50 IC H4 C1 C2 H7 1.09 110.70 59.18 110.70 1.09 IC H4 C1 C2 H8 1.09 110.70 -59.18 110.70 1.09 IC C1 C2 O3 H9 1.53 109.50 180.00 120.00 0.96 IC H7 C2 O3 H9 1.09 109.50 -58.46 120.00 0.96 IC H8 C2 O3 H9 1.09 109.50 58.46 120.00 0.96 IC C1 C2 O3 H10 1.53 109.50 48.15 120.00 0.96 IC C2 H9 *O3 H10 1.50 120.00 138.21 104.50 0.96 patch first none last none
PRES DLA -0.27 ATOM C2 CT2 0.00 ATOM QQL QQH 0.00 ATOM C1 CT3 -0.36 ATOM MML QQH 0.09 BOND C2 QQL BOND C1 MML ANGLE QQL C2 C1 ANGLE MML C1 C2
PRES DLP 0.23 ATOM C2 CT2 0.50 ATOM QQL QQH 0.00 ATOM C1 CT3 -0.36 ATOM MML QQH 0.09 BOND C2 QQL BOND C1 MML ANGLE QQL C2 C1 ANGLE MML C1 C2 END 1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 28a3 August 15, 2000 Copyright(c) 1984,1992 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.2.17(i686)@cub29.lobos.nih.gov Created on 2/21/ 1 at 21:28:46 by user: debdas
Maximum number of ATOMS: 60120, and RESidues: 72000 Current HEAP size: 10240000, and STACK size: 2000000
Processing passed argument "-p4pg" Processing passed argument "-p4wd" Processing passed argument "1:0.1" Parameter: 1 <- "0.1" RDTITL> * PROTONATED ETHANOL [CH3CH2OH2+] QM/MM CALCULATIONS RDTITL> *
CHARMM>
CHARMM> bomb -2
CHARMM>
CHARMM> open unit 1 read card name etoh_top.inp VOPEN> Attempting to open::etoh_top.inp:: OPNLGU> Unit 1 opened for READONLY access to etoh_top.inp
CHARMM> read rtf card unit 1 MAINIO> Residue topology file being read from unit 1. TITLE> *>> ALL-HYDROGEN TOPOLOGY FOR SMALL MODEL COMPOUNDS USED IN THE << TITLE> *>> DEVELOPMENT OF THE CHARMM22 PROTEIN ALL-HYDROGEN PARAMETERS << TITLE> *>>>>>>>>>>>>>>>>>>>>>>> JULY 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> *>>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<<< TITLE> *>>>>>>>> 410-706-7442 OR EMAIL: ALEX,MMIRIS.AB.UMD.EDU <<<<<<<<<< TITLE> *
CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP"
CHARMM>
CHARMM> open unit 1 read card name par_all22_prot_qmmm.inp VOPEN> Attempting to open::par_all22_prot_qmmm.inp:: OPNLGU> Unit 1 opened for READONLY access to par_all22_prot_qmmm.inp
CHARMM> read param card unit 1
PARAMETER FILE BEING READ FROM UNIT 1 TITLE> *>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>>>> JULY 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> *>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<< TITLE> *>>>>>> 410-706-7442 OR EMAIL: ALEX,MMIRIS.AB.UMD.EDU <<<<<<<<< TITLE> * PARRDR> WARNING: ATOMS IN BOND HT HT 0.00000 1.51390 DONT EXIST PARRDR> WARNING: ATOMS IN BOND OT HT 450.00000 0.95720 DONT EXIST PARRDR> WARNING: ATOMS IN ANGLE HT OT HT 55.00000 104.52000 DONT EXIST PARRDR> WARNING: ATOM FOR NBOND HT DOESNT EXIST PARRDR> Multiple terms for dihedral type: INDEX 443 CODE36924784 CT3 -OS -CD -OB PARRDR> Multiple terms for dihedral type: INDEX 441 CODE36919834 CT2 -OS -CD -OB PARRDR> Multiple terms for dihedral type: INDEX 434 CODE36611445 CP3 -N -C -O PARRDR> Multiple terms for dihedral type: INDEX 432 CODE36605676 CP2 -CP1 -C -O PARRDR> Multiple terms for dihedral type: INDEX 430 CODE36601545 CP1 -N -C -O PARRDR> Multiple terms for dihedral type: INDEX 421 CODE36486876 HB -CP1 -C -O PARRDR> Multiple terms for dihedral type: INDEX 406 CODE31833876 N -CP1 -C -NH1 PARRDR> Multiple terms for dihedral type: INDEX 404 CODE31734876 CP2 -CP1 -C -NH1 PARRDR> Multiple terms for dihedral type: INDEX 398 CODE31616076 HB -CP1 -C -NH1 PARRDR> Multiple terms for dihedral type: INDEX 387 CODE30715176 CP2 -CP1 -C -N PARRDR> Multiple terms for dihedral type: INDEX 381 CODE30596376 HB -CP1 -C -N PARRDR> Multiple terms for dihedral type: INDEX 353 CODE26632451 CT3 -NH1 -C -CP1 PARRDR> Multiple terms for dihedral type: INDEX 351 CODE26627501 CT2 -NH1 -C -CP1 PARRDR> Multiple terms for dihedral type: INDEX 349 CODE26622551 CT1 -NH1 -C -CP1 PARRDR> Multiple terms for dihedral type: INDEX 334 CODE25984001 CT2 -NH1 -C -CT3 PARRDR> Multiple terms for dihedral type: INDEX 332 CODE25979051 CT1 -NH1 -C -CT3 PARRDR> Multiple terms for dihedral type: INDEX 326 CODE25921463 HS -S -CT2 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 325 CODE25921463 HS -S -CT2 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 323 CODE25876301 H -OH1 -CT2 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 322 CODE25876301 H -OH1 -CT2 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 320 CODE25876300 H -OH1 -CT1 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 319 CODE25876300 H -OH1 -CT1 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 311 CODE25865201 CT1 -NH1 -C -CT2 PARRDR> Multiple terms for dihedral type: INDEX 306 CODE25762451 H -OH1 -CT2 -CT2 PARRDR> Multiple terms for dihedral type: INDEX 305 CODE25762451 H -OH1 -CT2 -CT2 PARRDR> Multiple terms for dihedral type: INDEX 295 CODE25698713 HS -S -CT2 -CT1 PARRDR> Multiple terms for dihedral type: INDEX 294 CODE25698713 HS -S -CT2 -CT1 PARRDR> Multiple terms for dihedral type: INDEX 292 CODE25653551 H -OH1 -CT2 -CT1 PARRDR> Multiple terms for dihedral type: INDEX 291 CODE25653551 H -OH1 -CT2 -CT1 PARRDR> Multiple terms for dihedral type: INDEX 289 CODE25653550 H -OH1 -CT1 -CT1 PARRDR> Multiple terms for dihedral type: INDEX 288 CODE25653550 H -OH1 -CT1 -CT1 PARRDR> Multiple terms for dihedral type: INDEX 242 CODE12103275 CP2 -CP1 -CC -O PARRDR> Multiple terms for dihedral type: INDEX 240 CODE11984475 HB -CP1 -CC -O PARRDR> Multiple terms for dihedral type: INDEX 226 CODE 7598775 N -CP1 -CC -NH2 PARRDR> Multiple terms for dihedral type: INDEX 224 CODE 7499775 CP2 -CP1 -CC -NH2 PARRDR> Multiple terms for dihedral type: INDEX 222 CODE 7380975 HB -CP1 -CC -NH2 PARRDR> Multiple terms for dihedral type: INDEX 189 CODE 6311676 N -C -CP1 -N PARRDR> Multiple terms for dihedral type: INDEX 181 CODE 2446545 CP1 -C -N -CP3 PARRDR> Multiple terms for dihedral type: INDEX 179 CODE 2421795 CT3 -C -N -CP3 PARRDR> Multiple terms for dihedral type: INDEX 177 CODE 2416845 CT2 -C -N -CP3 PARRDR> Multiple terms for dihedral type: INDEX 175 CODE 2411895 CT1 -C -N -CP3 PARRDR> Multiple terms for dihedral type: INDEX 169 CODE 2154495 CP1 -C -N -CP1 PARRDR> Multiple terms for dihedral type: INDEX 167 CODE 2129745 CT3 -C -N -CP1 PARRDR> Multiple terms for dihedral type: INDEX 165 CODE 2124795 CT2 -C -N -CP1 PARRDR> Multiple terms for dihedral type: INDEX 163 CODE 2119845 CT1 -C -N -CP1 PARRDR> Multiple terms for dihedral type: INDEX 132 CODE 1604123 CT3 -CT2 -CPH1-CPH1 PARRDR> Multiple terms for dihedral type: INDEX 131 CODE 1604123 CT3 -CT2 -CPH1-CPH1 PARRDR> Multiple terms for dihedral type: INDEX 128 CODE 1594223 CT1 -CT2 -CPH1-CPH1 PARRDR> Multiple terms for dihedral type: INDEX 127 CODE 1594223 CT1 -CT2 -CPH1-CPH1 PARRDR> Multiple terms for dihedral type: INDEX 120 CODE 1488403 CT3 -SM -SM -CT3 PARRDR> Multiple terms for dihedral type: INDEX 119 CODE 1488403 CT3 -SM -SM -CT3 PARRDR> Multiple terms for dihedral type: INDEX 117 CODE 1488263 CT3 -CT2 -S -CT3 PARRDR> Multiple terms for dihedral type: INDEX 115 CODE 1486451 CT3 -C -NH1 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 112 CODE 1483313 CT2 -CT2 -S -CT3 PARRDR> Multiple terms for dihedral type: INDEX 110 CODE 1481501 CT2 -C -NH1 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 107 CODE 1476551 CT1 -C -NH1 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 99 CODE 1369603 CT2 -SM -SM -CT2 PARRDR> Multiple terms for dihedral type: INDEX 98 CODE 1369603 CT2 -SM -SM -CT2 PARRDR> Multiple terms for dihedral type: INDEX 96 CODE 1367651 CT2 -C -NH1 -CT2 PARRDR> Multiple terms for dihedral type: INDEX 93 CODE 1362701 CT1 -C -NH1 -CT2 PARRDR> Multiple terms for dihedral type: INDEX 83 CODE 1253801 CT1 -C -NH1 -CT1 PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP"
CHARMM>
CHARMM> auto angle dihe AUTOGEN: All angles are removed and regenerated. AUTOGEN: All dihedrals are removed and regenerated. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 0 Number of residues = 0 Number of atoms = 0 Number of groups = 0 Number of bonds = 0 Number of angles = 0 Number of dihedrals = 0 Number of impropers = 0 Number of HB acceptors = 0 Number of HB donors = 0 Number of NB exclusions = 0 Total charge = 0.00000
CHARMM>
CHARMM> read sequ peto 1
CHARMM> generate peto setup NO PATCHING WILL BE DONE ON THE FIRST RESIDUE NO PATCHING WILL BE DONE ON THE LAST RESIDUE
***** LEVEL -1 WARNING FROM
GENPSF> Segment 1 has been generated. Its identifier is PETO. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 1 Number of atoms = 10 Number of groups = 2 Number of bonds = 9 Number of angles = 15 Number of dihedrals = 15 Number of impropers = 0 Number of HB acceptors = 0 Number of HB donors = 0 Number of NB exclusions = 0 Total charge = 1.00000
CHARMM>
CHARMM> print psf
PSF FILE MODULE CONTROL ARRAY : 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 * PROTONATED ETHANOL [CH3CH2OH2+] QM/MM CALCULATIONS * DATE: 2/21/ 1 21:28:47 CREATED BY USER: debdas *
NATOM NBOND NTHETA NPHI NIMPHI NNB NDON NACC NRES NSEG NGRP NST2 10 9 15 15 0 0 0 0 1 1 2 0 PARTITION OF SEGMENTS - NICTOT ARRAY AND SEGMENT IDENTIFIERS : SEGMENT NUMBER ID NRES NATOM NBOND NTHETA NPHI NIMPHI NNB NDON NACC TYPE 1 PETO 1
ATOM CHARACTERISTICS : ATOM TYPE CHARGE ATOM CODE COUNT OF MOVEMENT FLAG MASS EXCLUSIONS
RESIDUE 1 1 PETO TO 10 GROUP 1 TYPE 1 MOVE 0 TO 4 1 H4 0.0900 3 0 0 1.00800 2 H5 0.0900 3 0 0 1.00800 3 H6 0.0900 3 0 0 1.00800 4 C1 -0.2700 24 0 0 12.0110 GROUP 2 TYPE 2 MOVE 0 TO 10 5 H7 0.2500 3 0 0 1.00800 6 H8 0.2500 3 0 0 1.00800 7 C2 0.5000 23 0 0 12.0110 8 O3 0.0000 73 0 0 15.9990 9 H9 0.0000 1 0 0 1.00800 10 H10 0.0000 1 0 0 1.00800
BOND ARRAY (BY COLUMNS) : 1 4 4 4 4 7 7 7 8 8 7 1 2 3 5 6 8 9 10
THETA ARRAY (BY COLUMNS) : 1 1 1 1 2 2 3 4 4 4 5 5 6 7 7 9 4 4 4 4 4 4 7 7 7 7 7 7 8 8 8 2 3 7 3 7 7 5 6 8 6 8 8 9 10 10
PHI ARRAY (BY COLUMNS) : 1 1 1 1 2 2 2 3 3 3 4 4 5 5 6 6 4 4 4 4 4 4 4 4 4 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 5 6 8 5 6 8 5 6 8 9 10 9 10 9 10
IMPROPER TORSION ARRAY (BY COLUMNS) :
HYDROGEN DONOR ARRAYS :
HYDROGEN ACCEPTOR ARRAYS :
NON-BONDED EXCLUSION ARRAY :
CHARMM>
CHARMM> read coor card SPATIAL COORDINATES BEING READ FROM UNIT 5 RDTITL> * PROTONATED ETHANOL, COORDINATES FROM HF/6-31G RDTITL> * INITIAL COORS FROM PETHANOL_QUANTA_321G_2.COM RDTITL> * TOTAL ENERGY=- AU = - KCAL/MOL RDTITL> *
CHARMM>
CHARMM> !ic param CHARMM> ic build ALL POSSIBLE COORDINATES HAVE BEEN PLACED
CHARMM>
CHARMM> print psf
PSF FILE MODULE CONTROL ARRAY : 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 * PROTONATED ETHANOL [CH3CH2OH2+] QM/MM CALCULATIONS * DATE: 2/21/ 1 21:28:47 CREATED BY USER: debdas *
NATOM NBOND NTHETA NPHI NIMPHI NNB NDON NACC NRES NSEG NGRP NST2 10 9 15 15 0 0 0 0 1 1 2 0
PARTITION OF SEGMENTS - NICTOT ARRAY AND SEGMENT IDENTIFIERS : SEGMENT NUMBER ID NRES NATOM NBOND NTHETA NPHI NIMPHI NNB NDON NACC TYPE 1 PETO 1
ATOM CHARACTERISTICS : ATOM TYPE CHARGE ATOM CODE COUNT OF MOVEMENT FLAG MASS EXCLUSIONS
RESIDUE 1 1 PETO TO 10 GROUP 1 TYPE 1 MOVE 0 TO 4 1 H4 0.0900 3 0 0 1.00800 2 H5 0.0900 3 0 0 1.00800 3 H6 0.0900 3 0 0 1.00800 4 C1 -0.2700 24 0 0 12.0110 GROUP 2 TYPE 2 MOVE 0 TO 10 5 H7 0.2500 3 0 0 1.00800 6 H8 0.2500 3 0 0 1.00800 7 C2 0.5000 23 0 0 12.0110 8 O3 0.0000 73 0 0 15.9990 9 H9 0.0000 1 0 0 1.00800 10 H10 0.0000 1 0 0 1.00800
BOND ARRAY (BY COLUMNS) : 1 4 4 4 4 7 7 7 8 8 7 1 2 3 5 6 8 9 10
THETA ARRAY (BY COLUMNS) : 1 1 1 1 2 2 3 4 4 4 5 5 6 7 7 9 4 4 4 4 4 4 7 7 7 7 7 7 8 8 8 2 3 7 3 7 7 5 6 8 6 8 8 9 10 10
PHI ARRAY (BY COLUMNS) : 1 1 1 1 2 2 2 3 3 3 4 4 5 5 6 6 4 4 4 4 4 4 4 4 4 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 5 6 8 5 6 8 5 6 8 9 10 9 10 9 10
IMPROPER TORSION ARRAY (BY COLUMNS) :
HYDROGEN DONOR ARRAYS :
HYDROGEN ACCEPTOR ARRAYS :
NON-BONDED EXCLUSION ARRAY :
CHARMM>
CHARMM> ! add the link atoms by patching CHARMM>
CHARMM> PATCH DLP peto 1 setup
ATOM PETO PETO 1 QQL ADDED.
ATOM PETO PETO 1 MML ADDED.
Message from MAPIC: Atom numbers are changed. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 1 Number of atoms = 12 Number of groups = 2 Number of bonds = 11 Number of angles = 17 Number of dihedrals = 15 Number of impropers = 0 Number of HB acceptors = 0 Number of HB donors = 0 Number of NB exclusions = 0 Total charge = 1.00000
CHARMM> test psf
CHARMM> print psf
PSF FILE MODULE CONTROL ARRAY : 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 * PROTONATED ETHANOL [CH3CH2OH2+] QM/MM CALCULATIONS * DATE: 2/21/ 1 21:28:47 CREATED BY USER: debdas *
NATOM NBOND NTHETA NPHI NIMPHI NNB NDON NACC NRES NSEG NGRP NST2 12 11 17 15 0 0 0 0 1 1 2 0
PARTITION OF SEGMENTS - NICTOT ARRAY AND SEGMENT IDENTIFIERS : SEGMENT NUMBER ID NRES NATOM NBOND NTHETA NPHI NIMPHI NNB NDON NACC TYPE 1 PETO 1
ATOM CHARACTERISTICS : ATOM TYPE CHARGE ATOM CODE COUNT OF MOVEMENT FLAG MASS EXCLUSIONS
RESIDUE 1 1 PETO TO 12 GROUP 1 TYPE 1 MOVE 0 TO 5 1 H4 0.0900 3 0 0 1.00800 2 H5 0.0900 3 0 0 1.00800 3 H6 0.0900 3 0 0 1.00800 4 C1 -0.3600 24 0 0 12.0110 5 MML 0.0900 4 0 0 1.00800 GROUP 2 TYPE 2 MOVE 0 TO 12 6 H7 0.2500 3 0 0 1.00800 7 H8 0.2500 3 0 0 1.00800 8 C2 0.5000 23 0 0 12.0110 9 QQL 0.0000 4 0 0 1.00800 10 O3 0.0000 73 0 0 15.9990 11 H9 0.0000 1 0 0 1.00800 12 H10 0.0000 1 0 0 1.00800
BOND ARRAY (BY COLUMNS) : 1 4 4 4 4 4 8 8 8 8 10 10 1 2 3 5 8 6 7 9 10 11 12
THETA ARRAY (BY COLUMNS) : 1 1 1 1 2 2 3 4 4 4 5 6 6 7 8 8 9 11 4 4 4 4 4 4 8 8 8 4 8 8 8 10 10 8 10 2 3 8 3 8 8 6 7 10 8 7 10 10 11 12 4 12
PHI ARRAY (BY COLUMNS) : 1 1 1 1 2 2 2 3 3 3 4 4 6 6 7 7 4 4 4 4 4 4 4 4 4 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 10 10 10 10 10 10 6 7 10 6 7 10 6 7 10 11 12 11 12 11 12
IMPROPER TORSION ARRAY (BY COLUMNS) :
HYDROGEN DONOR ARRAYS :
HYDROGEN ACCEPTOR ARRAYS :
NON-BONDED EXCLUSION ARRAY :
CHARMM>
CHARMM>
CHARMM> !PLACE THE QM LINK ATOM CHARMM>
CHARMM> set dist 1.111 Parameter: DIST <- "1.111"
CHARMM>
CHARMM> ! coopying coor of C2 to QQL CHARMM> coor dupl sele bynu 8 end sele bynu 9 end SELRPN> 1 atoms have been selected out of 12 SELRPN> 1 atoms have been selected out of 12
CHARMM> !axis between C2 and C1 CHARMM> coor axis sele bynu 8 end sele bynu 4 end SELRPN> 1 atoms have been selected out of 12 SELRPN> 1 atoms have been selected out of 12 AXIS DEFINED FROM THE MAIN COORDINATES. XAXIs= -1.173800 YAXIs= -0.938200 ZAXIs= -0.000190 RAXIs= 1.502673
CHARMM> !translating QQL by 'DIST' A CHARMM> coor trans sele bynu 9 end axis dist @dist Parameter: DIST -> "1.111" SELRPN> 1 atoms have been selected out of 12 TRANSLATION VECTOR -0.867848 -0.693657 -0.000140 SELECTED COORDINATES TRANSLATED IN THE MAIN SET.
CHARMM>
CHARMM> !PLACE THE MM LINK ATOM CHARMM>
CHARMM> ! coopying coor of C1 to MML CHARMM> coor dupl sele bynu 4 end sele bynu 5 end SELRPN> 1 atoms have been selected out of 12 SELRPN> 1 atoms have been selected out of 12
CHARMM> !axis between C1 and C2 CHARMM> coor axis sele bynu 4 end sele bynu 8 end SELRPN> 1 atoms have been selected out of 12 SELRPN> 1 atoms have been selected out of 12 AXIS DEFINED FROM THE MAIN COORDINATES. XAXIs= 1.173800 YAXIs= 0.938200 ZAXIs= 0.000190 RAXIs= 1.502673 PHI WITH PREVIOUS AXIS: 180.000000
CHARMM> !translating MML by 'DIST' A CHARMM> coor trans sele bynu 5 end axis dist @dist Parameter: DIST -> "1.111" SELRPN> 1 atoms have been selected out of 12 TRANSLATION VECTOR 0.867848 0.693657 0.000140 SELECTED COORDINATES TRANSLATED IN THE MAIN SET.
CHARMM>
CHARMM> !select the QM region CHARMM>
CHARMM> define qm sele atom peto 1 c2 .or. atom peto 1 o3 - CHARMM> .or. atom peto 1 h7 .or. atom peto 1 h8 - CHARMM> .or. atom peto 1 h9 .or. atom peto 1 h10 - CHARMM> .or. atom peto 1 qql show end The following atoms are currently set: SEGId RESId RESName .. TYPEs .. PETO 1 PETO H7 H8 C2 QQL O3 H9 H10 SELRPN> 7 atoms have been selected out of 12
CHARMM>
CHARMM> !select the MM region CHARMM>
CHARMM> scalar wmain set @1 sele .not. qm end Parameter: 1 -> "0.1" SELRPN> 5 atoms have been selected out of 12
CHARMM>
CHARMM> scalar wmain show ( PETO PETO 1 H4 ) 0.10000 ( PETO PETO 1 H5 ) 0.10000 ( PETO PETO 1 H6 ) 0.10000 ( PETO PETO 1 C1 ) 0.10000 ( PETO PETO 1 MML ) 0.10000 ( PETO PETO 1 H7 ) 0.0000 ( PETO PETO 1 H8 ) 0.0000 ( PETO PETO 1 C2 ) 0.0000 ( PETO PETO 1 QQL ) 0.0000 ( PETO PETO 1 O3 ) 0.0000 ( PETO PETO 1 H9 ) 0.0000 ( PETO PETO 1 H10 ) 0.0000
CHARMM>
CHARMM> open write unit 1 card name ets.pdb VOPEN> Attempting to open::ets.pdb:: OPNLGU> Unit 1 opened for WRITE access to ets.pdb
CHARMM> coor write pdb unit 1 RDTITL> RDTITL> No title read.
CHARMM>
CHARMM> !anal on CHARMM> !anal term all CHARMM>
CHARMM> gamess remove blur sele qm end SELRPN> 7 atoms have been selected out of 12 GUKINT> REMOve: Classical energies within QM atoms are removed. GUKINT> No EXGRoup: QM/MM Elec. for link atom host only is removed. GUKINT> BLUR: Blurred charges will be used on some atoms. GUKINT> No QINP: Charges will be based on atomic numbers. ------GUKINT: Classical atoms excluded from the QM calculation: NONE. GUKINT: Quantum mechanical atoms: 6 PETO 1 PETO H7 7 PETO 1 PETO H8 8 PETO 1 PETO C2 10 PETO 1 PETO O3 11 PETO 1 PETO H9 12 PETO 1 PETO H10 GUKINT: Quantum mechanical link atoms: 9 PETO 1 PETO QQL ------GUKINT: ATOM( 6 1) has QNUC: -1000.00000 GUKINT: ATOM( 7 2) has QNUC: -1000.00000 GUKINT: ATOM( 8 3) has QNUC: -1000.00000 GUKINT: ATOM( 9 4) has QNUC: -1000.00000 GUKINT: ATOM( 10 5) has QNUC: -1000.00000 GUKINT: ATOM( 11 6) has QNUC: -1000.00000 GUKINT: ATOM( 12 7) has QNUC: -1000.00000 static lb: worker started static lb: worker started FINDEL: Quantum atom 6 PETO 1 PETO H7 assigned to element: H 1 FINDEL: Quantum atom 7 PETO 1 PETO H8 assigned to element: H 1 FINDEL: Quantum atom 8 PETO 1 PETO C2 assigned to element: C 6 FINDEL: Quantum atom 9 PETO 1 PETO QQL assigned to element: QQH 1 FINDEL: Quantum atom 10 PETO 1 PETO O3 assigned to element: O 8 FINDEL: Quantum atom 11 PETO 1 PETO H9 assigned to element: H 1 FINDEL: Quantum atom 12 PETO 1 PETO H10 assigned to element: H 1
The number of blurred MM charges = 5
GAMDFN> Some atoms will be treated quantum mechanically.
The number of quantum mechanical atoms = 7 The number of molecular mechanical atoms = 5 The number of MM atoms excluded from QM = 0 Of which the number of QM/MM link atoms = 1
Nuclear at type 1 charmm initialisation complete
CHARMM>
CHARMM> energy
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions.
Nuclear at type 1 Nutab 1 6 ian 1 1 1. Nutab 2 7 ian 2 1 1. Nutab 3 8 ian 3 6 6. Nutab 4 9 ian 4 1 1. Nutab 5 10 ian 5 8 8. Nutab 6 11 ian 6 1 1. Nutab 7 12 ian 7 1 1. Nutab 1 6 ian 1 1 1. Nutab 2 7 ian 2 1 1. Nutab 3 8 ian 3 6 6. Nutab 4 9 ian 4 1 1. Nutab 5 10 ian 5 8 8. Nutab 6 11 ian 6 1 1. Nutab 7 12 ian 7 1 1. Nutab 1 6 ian 1 1 1. Nutab 2 7 ian 2 1 1. Nutab 3 8 ian 3 6 6. Nutab 4 9 ian 4 1 1. Nutab 5 10 ian 5 8 8. Nutab 6 11 ian 6 1 1. Nutab 7 12 ian 7 1 1. Nutab 1 6 ian 1 1 1. Nutab 2 7 ian 2 1 1. Nutab 3 8 ian 3 6 6. Nutab 4 9 ian 4 1 1. Nutab 5 10 ian 5 8 8. Nutab 6 11 ian 6 1 1. Nutab 7 12 ian 7 1 1. Nutab 1 6 ian 1 1 1. Nutab 2 7 ian 2 1 1. Nutab 3 8 ian 3 6 6. Nutab 4 9 ian 4 1 1. Nutab 5 10 ian 5 8 8. Nutab 6 11 ian 6 1 1. Nutab 7 12 ian 7 1 1. Nutab 1 6 ian 1 1 1. Nutab 2 7 ian 2 1 1. Nutab 3 8 ian 3 6 6. Nutab 4 9 ian 4 1 1. Nutab 5 10 ian 5 8 8. Nutab 6 11 ian 6 1 1. Nutab 7 12 ian 7 1 1. Nutab 1 6 ian 1 1 1. Nutab 2 7 ian 2 1 1. Nutab 3 8 ian 3 6 6. Nutab 4 9 ian 4 1 1. Nutab 5 10 ian 5 8 8. Nutab 6 11 ian 6 1 1. Nutab 7 12 ian 7 1 1. Nutab 1 6 ian 1 1 1. Nutab 2 7 ian 2 1 1. Nutab 3 8 ian 3 6 6. Nutab 4 9 ian 4 1 1. Nutab 5 10 ian 5 8 8. Nutab 6 11 ian 6 1 1. Nutab 7 12 ian 7 1 1. Nutab 1 6 ian 1 1 1. Nutab 2 7 ian 2 1 1. Nutab 3 8 ian 3 6 6. Nutab 4 9 ian 4 1 1. Nutab 5 10 ian 5 8 8. Nutab 6 11 ian 6 1 1. Nutab 7 12 ian 7 1 1. Nutab 1 6 ian 1 1 1. Nutab 2 7 ian 2 1 1. Nutab 3 8 ian 3 6 6. Nutab 4 9 ian 4 1 1. Nutab 5 10 ian 5 8 8. Nutab 6 11 ian 6 1 1. Nutab 7 12 ian 7 1 1. Nutab 1 6 ian 1 1 1. Nutab 2 7 ian 2 1 1. Nutab 3 8 ian 3 6 6. Nutab 4 9 ian 4 1 1. Nutab 5 10 ian 5 8 8. Nutab 6 11 ian 6 1 1. Nutab 7 12 ian 7 1 1. Nutab 1 6 ian 1 1 1. Nutab 2 7 ian 2 1 1. Nutab 3 8 ian 3 6 6. Nutab 4 9 ian 4 1 1. Nutab 5 10 ian 5 8 8. Nutab 6 11 ian 6 1 1. Nutab 7 12 ian 7 1 1. EANGLFS> Warning: Angle 7 is almost linear. Derivatives may be affected for atoms: 5 4 8 EANGLFS> Warning: Angle 14 is almost linear. Derivatives may be affected for atoms: 9 8 4 ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ENER QUANTUM: QMELec QMVDw ------ENER> 0 -72347.69441 0.00000 137.07511 ENER INTERN> 0.92890 0.99446 0.19587 0.07355 0.00000 ENER EXTERN> -0.15820 0.00000 0.00000 0.00000 0.00000 ENER QUANTM> -72349.72900 0.00000 ------
CHARMM>
Parallel load balance (sec.): Node Eext Eint Wait Comm List Integ Total 0 0.0 2.4 0.0 0.0 0.0 0.0 2.4 $$$$$$ New timer profile $$$$$ Energy time 2.29000 Other: 0.00000 Dynamics total 2.29000 Other: 0.00000 Total time 3.77000 Other: 1.48000
NORMAL TERMINATION BY END OF FILE MAXIMUM STACK SPACE USED IS 72000 STACK CURRENTLY IN USE IS 0 MOST SEVERE WARNING WAS AT LEVEL -1 HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 176 MAXIMUM SPACE USED IS 4618 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10239824 NEXT: 0
$$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 3.89 SECONDS CPU TIME: 3.77 SECONDS * Energetic Profile Analysis of the Reaction Pathway * H. Lee Woodcock 8/31/2001 * bomlev -4
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!OPEN STREAM FILES AND READ INITIAL COORDINATES!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! stream "toppar27_setup.strm" open read card unit 50 name "a1.replica.psf" read psf card unit 50
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!DO THE QM/MM ENERGY CALCULATION!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!------envi qchemexe "qchem" envi qchemcnt "qchem.inp" envi qcheminp "q1.inp" envi qchemout "q1.out" !------
qchem remove noguess sele resn PRE .and. segid A* end !! SELECT THE QUANTUM REGION YOU WANT TO COMPUTE
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!COMPUTE THE ENERGY OF EACH REPLICA!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!read coor file ifile 284 unit 50 name "constrained_mini_qm_04.dcd"
open read card unit 32 name "constrained_mini_qm_05.crd" read coor card unit 32
open write file unit 37 name "constrained_mini_431g.dcd" mini abnr nstep 500 nprint 1 tolgrd 0.02 nsavc 1 iuncrd 37 - cdie cutnb 14.0 ctofnb 12.0 shift vshift atom
open write card unit 32 name "constrained_mini_431g.crd" write coor card unit 32 stop
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 5 process started 7 process started 1 process started 3 process started 0 process started 4 process started 6 process started 2 process started 1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 32a2 February 15, 2005 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.4.20-8smp(i686)@n95.lobos.nih.gov[+ 7] Created on 7/29/ 5 at 11:23:31 by user: hlwood
Maximum number of ATOMS: 240480, and RESidues: 60120 Current HEAP size: 10240000, and STACK size: 2000000
Processing passed argument "-p4pg" Processing passed argument "-p4wd" RDTITL> * ENERGETIC PROFILE ANALYSIS OF THE REACTION PATHWAY RDTITL> * H. LEE WOODCOCK 8/31/2001 RDTITL> *
CHARMM>
CHARMM> bomlev -4
CHARMM>
CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!OPEN STREAM FILES AND READ INITIAL COORDINATES!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM>
CHARMM>
CHARMM> stream "toppar27_setup.strm" VOPEN> Attempting to open::toppar27_setup.strm:: OPNLGU> Unit 99 opened for READONLY access to toppar27_setup.strm
INPUT STREAM SWITCHING TO UNIT 99 RDTITL> * READ IN CHARMM PARAMETER SET 27 FOR PROTEINS RDTITL> * H. LEE WOODCOCK 6/15/2001 RDTITL> * Parameter: IN1 <- ""
CHARMM>
CHARMM>
CHARMM> open unit 1 read card name "top_all22_prot.inp" VOPEN> Attempting to open::top_all22_prot.inp:: OPNLGU> Unit 1 opened for READONLY access to top_all22_prot.inp
CHARMM> read rtf unit 1 card MAINIO> Residue topology file being read from unit 1. TITLE> *>>>>>>>>CHARMM22 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>> DECEMBER 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: WWW.CHARMM.ORG TITLE> * PARAMETER SET DISCUSSION FORUM TITLE> *
CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP"
CHARMM>
CHARMM> open unit 1 read card name "prephenate_top.inp" VOPEN> Attempting to open::prephenate_top.inp:: OPNLGU> Unit 1 opened for READONLY access to prephenate_top.inp
CHARMM> read rtf append unit 1 card MAINIO> Residue topology file being read from unit 1. TITLE> * MANUALLY GENERATED RTF FILE FOR THE PREPHENATE MOLECULE TITLE> * H. LEE WOODCOCK 6/18/2001 TITLE> * WARNING from DECODI -- Zero length string being converted to 0 RTFRDR> WARNING: Version number is NOT specified.
CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP"
CHARMM>
CHARMM> open unit 1 read card name "chorismate_top.inp" VOPEN> Attempting to open::chorismate_top.inp:: OPNLGU> Unit 1 opened for READONLY access to chorismate_top.inp
CHARMM> read rtf append unit 1 card MAINIO> Residue topology file being read from unit 1. TITLE> * MANUALLY GENERATED RTF FILE FOR THE CHORISMATE MOLECULE TITLE> * H. LEE WOODCOCK 6/18/2001 TITLE> * WARNING from DECODI -- Zero length string being converted to 0 RTFRDR> WARNING: Version number is NOT specified.
CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP"
CHARMM>
CHARMM> open unit 2 read card name "par_all22_prot.inp" VOPEN> Attempting to open::par_all22_prot.inp:: OPNLGU> Unit 2 opened for READONLY access to par_all22_prot.inp
CHARMM> read param unit 2 card
PARAMETER FILE BEING READ FROM UNIT 2 TITLE> *>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>> DECEMBER 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: WWW.CHARMM.ORG TITLE> * PARAMETER SET DISCUSSION FORUM TITLE> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM> close unit 2 VCLOSE: Closing unit 2 with status "KEEP"
CHARMM>
CHARMM> open unit 2 read card name "add_prephenate_params.prm" VOPEN> Attempting to open::add_prephenate_params.prm:: OPNLGU> Unit 2 opened for READONLY access to add_prephenate_params.prm
CHARMM> read param append unit 2 card
PARAMETER FILE BEING READ FROM UNIT 2 TITLE> * EXTRA PARAMETERS FOR PREPHENATE TITLE> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM> close unit 2 VCLOSE: Closing unit 2 with status "KEEP"
CHARMM>
CHARMM> open unit 2 read card name "add_chorismate_params.prm" VOPEN> Attempting to open::add_chorismate_params.prm:: OPNLGU> Unit 2 opened for READONLY access to add_chorismate_params.prm
CHARMM> read param append unit 2 card
PARAMETER FILE BEING READ FROM UNIT 2 TITLE> * EXTRA PARAMETERS FOR PREPHENATE TITLE> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM> close unit 2 VCLOSE: Closing unit 2 with status "KEEP"
CHARMM>
CHARMM>
CHARMM> return VCLOSE: Closing unit 99 with status "KEEP"
RETURNING TO INPUT STREAM 5
CHARMM>
CHARMM> open read card unit 31 name "pre-dyna.cpt.weak.psf" VOPEN> Attempting to open::pre-dyna.cpt.weak.psf:: OPNLGU> Unit 31 opened for READONLY access to pre-dyna.cpt.weak.psf
CHARMM> read psf card unit 31 MAINIO> Protein structure file being read from unit 31. TITLE> *COORDS AFTER FIRST DYNAMICS RUN TITLE> * DATE: 7/ 5/ 1 6:30:34 CREATED BY USER: hlwood TITLE> * PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 5 Number of residues = 3274 Number of atoms = 14516 Number of groups = 4582 Number of bonds = 14554 Number of angles = 13481 Number of dihedrals = 15384 Number of impropers = 955 Number of cross-terms = 0 Number of HB acceptors = 3459 Number of HB donors = 627 Number of NB exclusions = 0 Total charge = -15.00000
CHARMM>
CHARMM> open read card unit 32 name "pre-mini-prot.crd" VOPEN> Attempting to open::pre-mini-prot.crd:: OPNLGU> Unit 32 opened for READONLY access to pre-mini-prot.crd
CHARMM> read coor card unit 32 comp SPATIAL COORDINATES BEING READ FROM UNIT 32 TITLE> * SETUP OF TEST JOB : CHORISMATE MUTASE W/ 3 PREPHENATES TITLE> * H. LEE WOODCOCK 6/15/2001 TITLE> * DATE: 9/ 5/ 1 16:51:58 CREATED BY USER: HLWOODC TITLE> *
CHARMM>
CHARMM> open read card unit 33 name "chr-mini-prot.crd" VOPEN> Attempting to open::chr-mini-prot.crd:: OPNLGU> Unit 33 opened for READONLY access to chr-mini-prot.crd
CHARMM> read coor ignore unit 33 SPATIAL COORDINATES BEING READ FROM UNIT 33 TITLE> * SETUP OF TEST JOB : CHORISMATE MUTASE W/ 3 PREPHENATES TITLE> * H. LEE WOODCOCK 6/15/2001 TITLE> * DATE: 9/ 4/ 1 20:23:42 CREATED BY USER: HLWOODC TITLE> *
CHARMM>
CHARMM>
CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!BEST FIT THE END POINTS OF THE PATHWAY!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM>
CHARMM> coor orient mass comp
ORIENT THE COORDINATES TO ALIGN WITH AXIS
MOMENTS **************** -69113.55506436 55496.93253194 **************** 69468.30301882 **************** Transpose of the rotation matrix 0.850678 0.523951 0.042690 -0.438568 0.752129 -0.491894 -0.289837 0.399721 0.869608 CENTER OF ATOMS BEFORE TRANSLATION 0.32377 -0.01242 -0.01790 AXIS OF ROTATION IS -0.658742 -0.245677 0.711127 ANGLE IS 42.59
ALL COORDINATES ORIENTED IN THE COMPARISON SET BASED ON SELECTED ATOMS.
CHARMM> coor orient rms mass CENTER OF ATOMS BEFORE TRANSLATION 0.32276 -0.01193 -0.01831 CENTER OF REFERENCE COORDINATE SET 0.00000 0.00000 0.00000 NET TRANSLATION OF ROTATED ATOMS -0.32276 0.01193 0.01831 ROTATION MATRIX 0.850719 -0.438502 -0.289817 0.523884 0.752157 0.399756 0.042694 -0.491910 0.869598 AXIS OF ROTATION IS 0.658811 0.245677 -0.711063 ANGLE IS 42.59
CENTER OF ROTATION 0.178029 0.272974 0.102649 SHIFT IS -0.222721
TOTAL SQUARE DIFF IS 5304.2180 DENOMINATOR IS 93286.2040 THUS RMS DIFF IS 0.238453 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS.
CHARMM>
CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!DEFINE THE BUFFER REGION TO INCLUDE FOR THE QM/MM CALCULATION!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM>
CHARMM> define close1 select .byres. ( ( resn PRE .and. resid 1 ) .around. 6.0 ) end SELRPN> 499 atoms have been selected out of 14516
CHARMM>
CHARMM> coor swap SELECTED COORDINATES SWAPPED.
CHARMM>
CHARMM> define close2 select .byres. ( ( resn PRE .and. resid 1 ) .around. 6.0 ) end SELRPN> 473 atoms have been selected out of 14516
CHARMM>
CHARMM> coor swap SELECTED COORDINATES SWAPPED.
CHARMM>
CHARMM> define close sele close1 .or. close2 end SELRPN> 518 atoms have been selected out of 14516
CHARMM>
CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!CREATE REPLICAS AND DELETE THE ORIGINAL REPLICATED REGION!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM>
CHARMM> replicate A nreplicate 21 select close end SELRPN> 518 atoms have been selected out of 14516 REPLIcate> Segments 6 to 26 have been generated. REPLIcate> Their identifiers are A 1 to 21 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 26 Number of residues = 4219 Number of atoms = 25394 Number of groups = 7711 Number of bonds = 25768 Number of angles = 32738 Number of dihedrals = 44007 Number of impropers = 2950 Number of cross-terms = 0 Number of HB acceptors = 4509 Number of HB donors = 1782 Number of NB exclusions = 0 Total charge = 6.00000
CHARMM>
CHARMM> dele atom sele close end SELRPN> 518 atoms have been selected out of 25394
Message from MAPIC: Atom numbers are changed.
Message from MAPIC: 45 residues deleted. DELTIC: 534 bonds deleted DELTIC: 917 angles deleted DELTIC: 1363 dihedrals deleted DELTIC: 95 improper dihedrals deleted DELTIC: 55 donors deleted DELTIC: 50 acceptors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 26 Number of residues = 4174 Number of atoms = 24876 Number of groups = 7562 Number of bonds = 25234 Number of angles = 31821 Number of dihedrals = 42644 Number of impropers = 2855 Number of cross-terms = 0 Number of HB acceptors = 4459 Number of HB donors = 1727 Number of NB exclusions = 0 Total charge = 5.00000
CHARMM>
CHARMM> !open write card unit 51 name "replica.psf" CHARMM> !write psf card unit 51 CHARMM>
CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!READ IN STREAM FILES TO DO THE ANALYSIS!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM>
CHARMM> stream "replica-psf.str" !! WRITE NEW PSF WITH ONLY 1 REPLICATED REGION VOPEN> Attempting to open::replica-psf.str:: OPNLGU> Unit 99 opened for READONLY access to replica-psf.str
INPUT STREAM SWITCHING TO UNIT 99 RDTITL> RDTITL> No title read. Parameter: IN1 <- ""
CHARMM>
CHARMM> dele atom sele segid A* .and. .not. segid A1 end SELRPN> 10360 atoms have been selected out of 24876
Message from MAPIC: Atom numbers are changed.
Message from MAPIC: 900 residues deleted.
Message from MAPIC: 20 segments deleted. REPLIcate> Segments 6 to 26 have been generated. DELTIC: 10680 bonds deleted REPLIcate> Their identifiers are A 1 to 21 DELTIC: 18340 angles deleted DELTIC: 27260 dihedrals deleted DELTIC: 1900 improper dihedrals deleted DELTIC: 1100 donors deleted DELTIC: 1000 acceptors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 6 Number of residues = 3274 Number of atoms = 14516 Number of groups = 4582 Number of bonds = 14554 Number of angles = 13481 Number of dihedrals = 15384 Number of impropers = 955 Number of cross-terms = 0 Number of HB acceptors = 3459 Number of HB donors = 627 Number of NB exclusions = 0 Total charge = -15.00000
CHARMM>
CHARMM> open write card unit 51 name "A1.replica.psf" VOPEN> Attempting to open::a1.replica.psf:: OPNLGU> Unit 51 opened for WRITE access to a1.replica.psf
CHARMM> write psf card unit 51 RDTITL> RDTITL> No title read. REPLIcate> Segments 6 to 26 have been generated. REPLIcate> Their identifiers are A 1 to 21 REPLIcate> Segments 6 to 26 have been generated. REPLIcate> Segments 6 to 26 have been generated. REPLIcate> Their identifiers are A 1 to 21 REPLIcate> Their identifiers are A 1 to 21 REPLIcate> Segments 6 to 26 have been generated. REPLIcate> Their identifiers are A 1 to 21 REPLIcate> Segments 6 to 26 have been generated. REPLIcate> Their identifiers are A 1 to 21 REPLIcate> Segments 6 to 26 have been generated. REPLIcate> Their identifiers are A 1 to 21
CHARMM>
CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM>
CHARMM>
VCLOSE: Closing unit 99 with status "KEEP"
RETURNING TO INPUT STREAM 5
CHARMM> !stream "write-coords.str" !! WRITE COORDINATES OF EACH REPLICATES REGION CHARMM> !stream "cons_mini.str" CHARMM> stream "energy.str" !! DO THE QM/MM ENERGY CALCULATION OF EACH REPLICA VOPEN> Attempting to open::energy.str:: OPNLGU> Unit 99 opened for READONLY access to energy.str
INPUT STREAM SWITCHING TO UNIT 99 RDTITL> RDTITL> No title read. Parameter: IN1 <- ""
CHARMM>
CHARMM> replica reset !! MUST REST THE REPLICA COMMAND Replica: Reset. A single (primary) subsystem is assumed.
CHARMM>
CHARMM> open read card unit 50 name "a1.replica.psf" OPNLGU> ***** WARNING ***** another unit is already assigned to the file - it will be disconnected first. VCLOSE: Closing unit 51 with status "KEEP" VOPEN> Attempting to open::a1.replica.psf:: OPNLGU> Unit 50 opened for READONLY access to a1.replica.psf
CHARMM> read psf card unit 50 MAINIO> Protein structure file being read from unit 50. TITLE> * ENERGETIC PROFILE ANALYSIS OF THE REACTION PATHWAY TITLE> * H. LEE WOODCOCK 8/31/2001 TITLE> * DATE: 7/29/ 5 11:23:35 CREATED BY USER: hlwood TITLE> * Replica: Reset. A single (primary) subsystem is assumed. Replica: Reset. A single (primary) subsystem is assumed. Replica: Reset. A single (primary) subsystem is assumed. Replica: Reset. A single (primary) subsystem is assumed. Replica: Reset. A single (primary) subsystem is assumed. Replica: Reset. A single (primary) subsystem is assumed. Replica: Reset. A single (primary) subsystem is assumed. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 6 Number of residues = 3274 Number of atoms = 14516 Number of groups = 4582 Number of bonds = 14554 Number of angles = 13481 Number of dihedrals = 15384 Number of impropers = 955 Number of cross-terms = 0 Number of HB acceptors = 3459 Number of HB donors = 627 Number of NB exclusions = 0 Total charge = -15.00000
CHARMM>
CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM>
CHARMM> !open write card unit 55 name esteps.dat CHARMM>
CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!DO THE QM/MM ENERGY CALCULATION!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM>
CHARMM> !------CHARMM> envi qchemexe "qchem"
CHARMM> envi qchemcnt "qchem.inp"
CHARMM> envi qcheminp "q1.inp"
CHARMM> envi qchemout "q1.out"
CHARMM> !envi PBS_NODEFILE "qchosts" CHARMM> !system "hostname > qchosts" CHARMM> !------CHARMM>
CHARMM> qchem remove noguess sele resn PRE .and. segid A* end !! SELECT THE QUANTUM REGION YOU WANT TO COMPUTE SELRPN> 24 atoms have been selected out of 14516 QCHEM> REMOve: Classical energies within QM atoms are removed. QCHEM> No EXGRoup: QM/MM Elec. for link atom host only is removed. QCHEM> NOGUess: Initial guess obtained from previous step. QCHEM> No QINP: Charges will be based on atomic numbers. QCHEM: Classical atoms excluded from the QM calculation: NONE. QCHEM: Quantum mechanical atoms: 14442 A1 1 PRE O4 14443 A1 1 PRE H4 14444 A1 1 PRE C1 14445 A1 1 PRE C2 14446 A1 1 PRE H1 14447 A1 1 PRE C3 14448 A1 1 PRE H2 14449 A1 1 PRE C4 14450 A1 1 PRE H3 14451 A1 1 PRE C5 14452 A1 1 PRE H5 14453 A1 1 PRE C6 14454 A1 1 PRE H6 14455 A1 1 PRE C7 14456 A1 1 PRE 1O7 14457 A1 1 PRE 2O7 14458 A1 1 PRE C8 14459 A1 1 PRE H7 14460 A1 1 PRE H8 14461 A1 1 PRE C1' 14462 A1 1 PRE O1' 14463 A1 1 PRE C2' 14464 A1 1 PRE 1O2' 14465 A1 1 PRE 2O2' QCHEM: Quantum mechanical link atoms: NONE. ------
CHARMM>
CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!COMPUTE THE ENERGY OF EACH REPLICA!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM>
CHARMM> !read coor file ifile 284 unit 50 name "constrained_mini_qm_04.dcd" CHARMM>
CHARMM> open read card unit 32 name "constrained_mini_qm_05.crd" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 32 with status "KEEP" VOPEN> Attempting to open::constrained_mini_qm_05.crd:: OPNLGU> Unit 32 opened for READONLY access to constrained_mini_qm_05.crd
CHARMM> read coor card unit 32 SPATIAL COORDINATES BEING READ FROM UNIT 32 TITLE> * ENERGETIC PROFILE ANALYSIS OF THE REACTION PATHWAY TITLE> * H. LEE WOODCOCK 8/31/2001 TITLE> * DATE: 7/27/ 5 7:56:12 CREATED BY USER: HLWOOD TITLE> *
CHARMM>
CHARMM> !energy CHARMM> !test first tol 0.00 select resn PRE .and. segid A* end CHARMM> !test first tol 0.00 select resid 2 .and. segid A1 show end CHARMM>
CHARMM> !coor force comp CHARMM> !open write card unit 32 name "qm_mm_force.cor" CHARMM> !write coor card unit 32 comp CHARMM>
CHARMM> !open read card unit 51 name "constrained_mini_qm_03.crd" CHARMM> !read coor ignore unit 51 CHARMM>
CHARMM> open write file unit 37 name "constrained_mini_431g.dcd" VOPEN> Attempting to open::constrained_mini_431g.dcd:: OPNLGU> Unit 37 opened for WRITE access to constrained_mini_431g.dcd
CHARMM> mini abnr nstep 500 nprint 1 tolgrd 0.02 nsavc 1 iuncrd 37 - CHARMM> cdie cutnb 14.0 ctofnb 12.0 shift vshift atom
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSHIft BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions.
General atom nonbond list generation found: 874085 ATOM PAIRS WERE FOUND FOR ATOM LIST 49907 GROUP PAIRS REQUIRED ATOM SEARCHES
ABNER> An energy minimization has been requested.
EIGRNG = 0.0005000 MINDIM = 5 NPRINT = 1 NSTEP = 500 PSTRCT = 0.0000000 SDSTP = 0.0200000 STPLIM = 1.0000000 STRICT = 0.1000000 TOLFUN = 0.0000000 TOLGRD = 0.0200000 TOLITR = 100 TOLSTP = 0.0000000 FMEM = 0.0000000 QCHEM> QCHEM> Q-Chem Job Parameters QCHEM> ------QCHEM> exchange hf QCHEM> basis 4-31g QCHEM> FINDEL: Quantum atom 14442 A1 1 PRE O4 assigned to element: O 8 FINDEL: Quantum atom 14443 A1 1 PRE H4 assigned to element: H 1 FINDEL: Quantum atom 14444 A1 1 PRE C1 assigned to element: C 6 FINDEL: Quantum atom 14445 A1 1 PRE C2 assigned to element: C 6 FINDEL: Quantum atom 14446 A1 1 PRE H1 assigned to element: H 1 FINDEL: Quantum atom 14447 A1 1 PRE C3 assigned to element: C 6 FINDEL: Quantum atom 14448 A1 1 PRE H2 assigned to element: H 1 FINDEL: Quantum atom 14449 A1 1 PRE C4 assigned to element: C 6 FINDEL: Quantum atom 14450 A1 1 PRE H3 assigned to element: H 1 FINDEL: Quantum atom 14451 A1 1 PRE C5 assigned to element: C 6 FINDEL: Quantum atom 14452 A1 1 PRE H5 assigned to element: H 1 FINDEL: Quantum atom 14453 A1 1 PRE C6 assigned to element: C 6 FINDEL: Quantum atom 14454 A1 1 PRE H6 assigned to element: H 1 FINDEL: Quantum atom 14455 A1 1 PRE C7 assigned to element: C 6 FINDEL: Quantum atom 14456 A1 1 PRE 1O7 assigned to element: O 8 FINDEL: Quantum atom 14457 A1 1 PRE 2O7 assigned to element: O 8 FINDEL: Quantum atom 14458 A1 1 PRE C8 assigned to element: C 6 FINDEL: Quantum atom 14459 A1 1 PRE H7 assigned to element: H 1 FINDEL: Quantum atom 14460 A1 1 PRE H8 assigned to element: H 1 FINDEL: Quantum atom 14461 A1 1 PRE C1' assigned to element: C 6 FINDEL: Quantum atom 14462 A1 1 PRE O1' assigned to element: O 8 FINDEL: Quantum atom 14463 A1 1 PRE C2' assigned to element: C 6 FINDEL: Quantum atom 14464 A1 1 PRE 1O2' assigned to element: O 8 FINDEL: Quantum atom 14465 A1 1 PRE 2O2' assigned to element: O 8 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI QUANTUM: QMELec QMVDw ------MINI> 0-573591.35370 0.00000 0.43182 0.00000 MINI INTERN> 1775.63059 1881.05620 84.03465 1539.57392 28.62466 MINI EXTERN> 4505.43813 -61680.91104 0.00000 0.00000 0.00000 MINI QUANTM> -521724.80081 0.00000 ------MINI> 1-573592.72914 1.37544 0.25082 0.02000 MINI INTERN> 1775.80751 1881.06651 84.04362 1539.58036 28.62454 MINI EXTERN> 4505.39236 -61680.82971 0.00000 0.00000 0.00000 MINI QUANTM> -521726.41433 0.00000 ------MINI> 2-573593.84232 1.11318 0.16940 0.02400 MINI INTERN> 1776.02337 1881.05160 84.01525 1539.59864 28.62351 MINI EXTERN> 4505.30583 -61680.65098 0.00000 0.00000 0.00000 MINI QUANTM> -521727.80955 0.00000 ------MINI> 3-573594.21381 0.37149 0.26543 0.03600 MINI INTERN> 1775.86835 1880.98172 83.93605 1539.62681 28.62082 MINI EXTERN> 4505.10059 -61680.44618 0.00000 0.00000 0.00000 MINI QUANTM> -521727.90197 0.00000 ------MINI> 4-573594.67613 0.46232 0.26282 0.03240 MINI INTERN> 1776.25388 1880.98147 83.98350 1539.65646 28.62017 MINI EXTERN> 4505.31224 -61680.31677 0.00000 0.00000 0.00000 MINI QUANTM> -521729.16709 0.00000 ------MINI> 5-573594.88781 0.21168 0.28752 0.02916 MINI INTERN> 1776.22621 1880.97406 83.92444 1539.68430 28.61956 MINI EXTERN> 4505.44844 -61680.19774 0.00000 0.00000 0.00000 MINI QUANTM> -521729.56707 0.00000 ------MINI> 6-573595.62293 0.73512 0.16584 0.02624 MINI INTERN> 1776.22529 1881.01090 83.87582 1539.75299 28.61876 MINI EXTERN> 4505.90104 -61679.91723 0.00000 0.00000 0.00000 MINI QUANTM> -521731.09050 0.00000 ------MINI> 7-573595.79908 0.17615 0.19075 0.02362 MINI INTERN> 1776.56113 1881.03370 83.97850 1539.80303 28.61896 MINI EXTERN> 4506.14268 -61679.75045 0.00000 0.00000 0.00000 MINI QUANTM> -521732.18662 0.00000 ------MINI> 8-573596.22211 0.42304 0.15621 0.02126 MINI INTERN> 1776.48824 1881.11644 83.93455 1539.89302 28.62025 MINI EXTERN> 4507.08064 -61679.44545 0.00000 0.00000 0.00000 MINI QUANTM> -521733.90980 0.00000 ------MINI> 9-573596.34052 0.11841 0.15828 0.01913 MINI INTERN> 1776.54896 1881.19142 83.91136 1539.93420 28.61958 MINI EXTERN> 4507.38455 -61679.15435 0.00000 0.00000 0.00000 MINI QUANTM> -521734.77624 0.00000 ------MINI> 10-573596.49527 0.15475 0.16983 0.01722 MINI INTERN> 1776.68288 1881.27948 83.93408 1540.00184 28.62009 MINI EXTERN> 4507.94833 -61678.89802 0.00000 0.00000 0.00000 MINI QUANTM> -521736.06397 0.00000 ------MINI> 11-573596.67282 0.17755 0.13733 0.01550 MINI INTERN> 1776.81378 1881.35721 83.96706 1540.05997 28.62021 MINI EXTERN> 4508.49054 -61678.63769 0.00000 0.00000 0.00000 MINI QUANTM> -521737.34389 0.00000 ------MINI> 12-573596.75554 0.08272 0.13200 0.01395 MINI INTERN> 1776.72344 1881.40745 83.92692 1540.09474 28.62002 MINI EXTERN> 4508.88864 -61678.41395 0.00000 0.00000 0.00000 MINI QUANTM> -521738.00280 0.00000 ------MINI> 13-573596.91179 0.15625 0.09563 0.01255 MINI INTERN> 1776.72318 1881.50352 83.91171 1540.14950 28.61991 MINI EXTERN> 4509.41159 -61678.04392 0.00000 0.00000 0.00000 MINI QUANTM> -521739.18729 0.00000 ------MINI> 14-573597.01699 0.10520 0.07266 0.01130 MINI INTERN> 1776.93584 1881.56323 83.97052 1540.18489 28.62070 MINI EXTERN> 4509.61719 -61677.83394 0.00000 0.00000 0.00000 MINI QUANTM> -521740.07543 0.00000 ------MINI> 15-573597.13327 0.11627 0.07717 0.01017 MINI INTERN> 1776.88581 1881.66491 83.95052 1540.24567 28.62158 MINI EXTERN> 4510.29700 -61677.39727 0.00000 0.00000 0.00000 MINI QUANTM> -521741.40148 0.00000 ------MINI> 16-573597.23565 0.10238 0.06031 0.00915 MINI INTERN> 1776.89335 1881.72184 83.95400 1540.27220 28.62256 MINI EXTERN> 4510.52002 -61677.07360 0.00000 0.00000 0.00000 MINI QUANTM> -521742.14602 0.00000 ------MINI> 17-573597.33626 0.10061 0.05900 0.00824 MINI INTERN> 1776.92670 1881.79362 83.96803 1540.30862 28.62455 MINI EXTERN> 4510.84757 -61676.67683 0.00000 0.00000 0.00000 MINI QUANTM> -521743.12853 0.00000 ------MINI> 18-573597.46416 0.12790 0.04658 0.00741 MINI INTERN> 1776.89789 1881.81407 83.97838 1540.31419 28.62725 MINI EXTERN> 4510.91717 -61676.34021 0.00000 0.00000 0.00000 MINI QUANTM> -521743.67291 0.00000 ------MINI> 19-573597.56983 0.10567 0.04981 0.00667 MINI INTERN> 1776.83471 1881.76525 83.99147 1540.27990 28.63036 MINI EXTERN> 4510.69422 -61676.13790 0.00000 0.00000 0.00000 MINI QUANTM> -521743.62784 0.00000 ------MINI> 20-573597.60411 0.03428 0.05089 0.00600 MINI INTERN> 1776.83560 1881.75120 83.99489 1540.26486 28.63075 MINI EXTERN> 4510.60641 -61676.03201 0.00000 0.00000 0.00000 MINI QUANTM> -521743.65580 0.00000 ------MINI> 21-573597.63352 0.02942 0.04528 0.00540 MINI INTERN> 1776.81115 1881.70142 83.99530 1540.23705 28.63051 MINI EXTERN> 4510.47260 -61676.08574 0.00000 0.00000 0.00000 MINI QUANTM> -521743.39582 0.00000 ------MINI> 22-573597.68144 0.04791 0.03188 0.00486 MINI INTERN> 1776.78972 1881.66912 83.98928 1540.21272 28.62932 MINI EXTERN> 4510.46383 -61676.04136 0.00000 0.00000 0.00000 MINI QUANTM> -521743.39408 0.00000 ------MINI> 23-573597.72537 0.04394 0.02547 0.00438 MINI INTERN> 1776.78163 1881.64269 83.98181 1540.18931 28.62710 MINI EXTERN> 4510.50839 -61676.01826 0.00000 0.00000 0.00000 MINI QUANTM> -521743.43804 0.00000 ------MINI> 24-573597.75274 0.02737 0.02694 0.00394 MINI INTERN> 1776.78420 1881.63300 83.97753 1540.17768 28.62555 MINI EXTERN> 4510.61017 -61675.98652 0.00000 0.00000 0.00000 MINI QUANTM> -521743.57436 0.00000 ------MINI> 25-573597.77997 0.02723 0.03078 0.00355 MINI INTERN> 1776.80738 1881.64909 83.97135 1540.18103 28.62332 MINI EXTERN> 4510.83633 -61675.95940 0.00000 0.00000 0.00000 MINI QUANTM> -521743.88909 0.00000 ------MINI> 26-573597.80102 0.02105 0.02500 0.00319 MINI INTERN> 1776.82885 1881.66609 83.96952 1540.18807 28.62246 MINI EXTERN> 4510.99017 -61675.91544 0.00000 0.00000 0.00000 MINI QUANTM> -521744.15074 0.00000 ------MINI> 27-573597.81585 0.01483 0.04575 0.00479 MINI INTERN> 1776.85419 1881.67450 83.97128 1540.19386 28.62220 MINI EXTERN> 4511.07924 -61675.86587 0.00000 0.00000 0.00000 MINI QUANTM> -521744.34525 0.00000 ------MINI> 28-573597.86272 0.04687 0.02090 0.00431 MINI INTERN> 1776.87494 1881.68469 83.97246 1540.20002 28.62204 MINI EXTERN> 4511.18515 -61675.75978 0.00000 0.00000 0.00000 MINI QUANTM> -521744.64224 0.00000 ------MINI> 29-573597.93398 0.07126 0.02225 0.00388 MINI INTERN> 1776.91575 1881.70010 83.97755 1540.21012 28.62189 MINI EXTERN> 4511.36842 -61675.48581 0.00000 0.00000 0.00000 MINI QUANTM> -521745.24201 0.00000 ------MINI> 30-573598.00942 0.07544 0.04589 0.00581 MINI INTERN> 1776.91736 1881.69532 83.98233 1540.20598 28.62112 MINI EXTERN> 4511.40986 -61675.08764 0.00000 0.00000 0.00000 MINI QUANTM> -521745.75374 0.00000 ------MINI> 31-573598.06791 0.05848 0.03137 0.00523 MINI INTERN> 1776.90256 1881.69760 83.98174 1540.20034 28.61940 MINI EXTERN> 4511.47847 -61674.84551 0.00000 0.00000 0.00000 MINI QUANTM> -521746.10251 0.00000 ------MINI> 32-573598.12689 0.05898 0.03495 0.00471 MINI INTERN> 1776.89466 1881.70803 83.98213 1540.19536 28.61682 MINI EXTERN> 4511.64972 -61674.41414 0.00000 0.00000 0.00000 MINI QUANTM> -521746.75948 0.00000 ------MINI> 33-573598.18936 0.06247 0.02226 0.00424 MINI INTERN> 1776.90292 1881.74068 83.98076 1540.20006 28.61379 MINI EXTERN> 4512.02275 -61674.04663 0.00000 0.00000 0.00000 MINI QUANTM> -521747.60367 0.00000 ------MINI> 34-573598.22654 0.03718 0.06405 0.00636 MINI INTERN> 1776.94784 1881.79172 83.98456 1540.22828 28.61110 MINI EXTERN> 4512.74895 -61673.47654 0.00000 0.00000 0.00000 MINI QUANTM> -521749.06244 0.00000 ------MINI> 35-573598.23432 0.00778 0.05878 0.00572 MINI INTERN> 1776.94707 1881.79497 83.98507 1540.22694 28.61094 MINI EXTERN> 4512.74623 -61673.49967 0.00000 0.00000 0.00000 MINI QUANTM> -521749.04588 0.00000 ------MINI> 36-573598.25637 0.02204 0.04817 0.00515 MINI INTERN> 1776.97384 1881.80969 83.98818 1540.24191 28.61063 MINI EXTERN> 4512.93710 -61673.38681 0.00000 0.00000 0.00000 MINI QUANTM> -521749.43090 0.00000 ------MINI> 37-573598.27516 0.01880 0.04511 0.00464 MINI INTERN> 1776.99879 1881.81859 83.99419 1540.25954 28.61057 MINI EXTERN> 4513.10133 -61673.23435 0.00000 0.00000 0.00000 MINI QUANTM> -521749.82384 0.00000 ------MINI> 38-573598.29459 0.01943 0.03742 0.00417 MINI INTERN> 1777.02014 1881.82176 84.00046 1540.27807 28.61114 MINI EXTERN> 4513.14701 -61673.25471 0.00000 0.00000 0.00000 MINI QUANTM> -521749.91846 0.00000 ------MINI> 39-573598.32370 0.02911 0.02102 0.00375 MINI INTERN> 1777.03776 1881.83268 84.00509 1540.30479 28.61067 MINI EXTERN> 4513.22951 -61673.16370 0.00000 0.00000 0.00000 MINI QUANTM> -521750.18050 0.00000 ------MINI> 40-573598.34168 0.01798 0.05632 0.00563 MINI INTERN> 1777.04029 1881.84835 84.00218 1540.33440 28.61041 MINI EXTERN> 4513.08105 -61673.20968 0.00000 0.00000 0.00000 MINI QUANTM> -521750.04867 0.00000 ------MINI> 41-573598.36140 0.01972 0.04828 0.00507 MINI INTERN> 1777.03546 1881.84613 84.00237 1540.34719 28.61031 MINI EXTERN> 4513.03580 -61673.17910 0.00000 0.00000 0.00000 MINI QUANTM> -521750.05955 0.00000 ------MINI> 42-573598.38186 0.02047 0.04229 0.00456 MINI INTERN> 1777.00664 1881.84015 83.99832 1540.35019 28.61117 MINI EXTERN> 4512.87869 -61673.19729 0.00000 0.00000 0.00000 MINI QUANTM> -521749.86973 0.00000 ------MINI> 43-573598.39058 0.00872 0.04203 0.00411 MINI INTERN> 1777.00138 1881.84294 83.99676 1540.35303 28.61151 MINI EXTERN> 4512.84134 -61673.19203 0.00000 0.00000 0.00000 MINI QUANTM> -521749.84551 0.00000 ------MINI> 44-573598.41362 0.02304 0.03356 0.00370 MINI INTERN> 1776.97618 1881.82891 83.99540 1540.34751 28.61308 MINI EXTERN> 4512.69169 -61673.18851 0.00000 0.00000 0.00000 MINI QUANTM> -521749.67790 0.00000 ------MINI> 45-573598.43037 0.01674 0.02808 0.00333 MINI INTERN> 1776.95469 1881.80635 83.99521 1540.32935 28.61461 MINI EXTERN> 4512.56503 -61673.18561 0.00000 0.00000 0.00000 MINI QUANTM> -521749.50999 0.00000 ------MINI> 46-573598.44495 0.01459 0.02290 0.00299 MINI INTERN> 1776.94044 1881.78343 83.99694 1540.31464 28.61563 MINI EXTERN> 4512.45824 -61673.17915 0.00000 0.00000 0.00000 MINI QUANTM> -521749.37512 0.00000 ------MINI> 47-573598.44651 0.00156 0.04589 0.00449 MINI INTERN> 1776.93171 1881.76798 83.99766 1540.30537 28.61537 MINI EXTERN> 4512.40516 -61673.18859 0.00000 0.00000 0.00000 MINI QUANTM> -521749.28117 0.00000 ------MINI> 48-573598.46265 0.01614 0.04003 0.00404 MINI INTERN> 1776.91888 1881.73622 83.99928 1540.28355 28.61550 MINI EXTERN> 4512.26273 -61673.19175 0.00000 0.00000 0.00000 MINI QUANTM> -521749.08704 0.00000 ------MINI> 49-573598.47562 0.01297 0.03347 0.00364 MINI INTERN> 1776.91873 1881.71982 83.99960 1540.27270 28.61432 MINI EXTERN> 4512.18741 -61673.19006 0.00000 0.00000 0.00000 MINI QUANTM> -521748.99813 0.00000 ------MINI> 50-573598.48954 0.01392 0.02385 0.00327 MINI INTERN> 1776.91912 1881.71070 83.99605 1540.26663 28.61225 MINI EXTERN> 4512.13234 -61673.18773 0.00000 0.00000 0.00000 MINI QUANTM> -521748.93889 0.00000 ------MINI> 51-573598.49356 0.00403 0.02752 0.00295 MINI INTERN> 1776.91560 1881.70629 83.99476 1540.26230 28.61169 MINI EXTERN> 4512.08257 -61673.19100 0.00000 0.00000 0.00000 MINI QUANTM> -521748.87577 0.00000 ------MINI> 52-573598.50290 0.00934 0.02455 0.00265 MINI INTERN> 1776.92389 1881.70940 83.99051 1540.26253 28.60956 MINI EXTERN> 4512.05844 -61673.18183 0.00000 0.00000 0.00000 MINI QUANTM> -521748.87541 0.00000 ------MINI> 53-573598.51587 0.01296 0.01621 0.00239 MINI INTERN> 1776.93295 1881.71432 83.98477 1540.26308 28.60734 MINI EXTERN> 4512.01332 -61673.16380 0.00000 0.00000 0.00000 MINI QUANTM> -521748.86784 0.00000 ------
ABNER> Minimization exiting with gradient tolerance ( 0.0200000) satisfied.
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ABNR EXTERN: VDWaals ELEC HBONds ASP USER ABNR QUANTUM: QMELec QMVDw ------ABNR> 53-573598.51587 0.01296 0.01621 0.00215 ABNR INTERN> 1776.93295 1881.71432 83.98477 1540.26308 28.60734 ABNR EXTERN> 4512.01332 -61673.16380 0.00000 0.00000 0.00000 ABNR QUANTM> -521748.86784 0.00000 ------
CHARMM>
CHARMM> open write card unit 32 name "constrained_mini_431g.crd" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 32 with status "KEEP" VOPEN> Attempting to open::constrained_mini_431g.crd:: OPNLGU> Unit 32 opened for WRITE access to constrained_mini_431g.crd
CHARMM> write coor card unit 32 RDTITL> RDTITL> No title read. VCLOSE: Closing unit 32 with status "KEEP"
CHARMM>
CHARMM> format
CHARMM>
CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM>
CHARMM>
VCLOSE: Closing unit 99 with status "KEEP"
RETURNING TO INPUT STREAM 5
CHARMM>
CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM>
CHARMM> STOP Parallel load balance (sec.): Node Eext Eint Wait Comm List Integ Total 0 5.0 5268.2 1.4 7.8 1.7 0.0 5284.1 1 5.1 0.3 5269.4 7.6 1.5 0.0 5283.9 2 5.0 0.4 5269.4 7.5 1.6 0.0 5283.8 3 5.0 0.4 5269.3 7.4 1.6 0.0 5283.7 4 5.0 0.4 5269.3 7.2 1.6 0.0 5283.4 5 5.1 0.4 5269.2 7.8 1.9 0.0 5284.3 6 5.0 0.4 5269.2 8.0 1.8 0.0 5284.5 7 5.0 0.4 5269.3 8.0 1.7 0.0 5284.3 PARALLEL> Average timing for all nodes: 8 5.0 658.8 4610.8 7.6 1.7 0.0 5284.0 VCLOSE: Closing unit 31 with status "KEEP" VCLOSE: Closing unit 33 with status "KEEP" VCLOSE: Closing unit 37 with status "KEEP" VCLOSE: Closing unit 50 with status "KEEP"
$$$$$$ New timer profile Local node$$$$$
Electrostatic & VDW 5.01163 Other: 0.00000 Nonbond force 5.01406 Other: 0.00243 Bond energy 0.04232 Other: 0.00000 Angle energy 0.05088 Other: 0.00000 Dihedral energy 0.05146 Other: 0.00000 Restraints energy 0.00024 Other: 0.00000 INTRNL energy 5270.58281 Other: 5270.43790 Comm force 10.27906 Other: 0.00000 Energy time 5285.90599 Other: 0.03007 Total time 5299.48554 Other: 13.57955
$$$$$$ Average profile $$$$$
Electrostatic & VDW 5.01740 Other: 0.00000 Nonbond force 5.02097 Other: 0.00934 Bond energy 0.06721 Other: 0.00000 Angle energy 0.06740 Other: 0.00000 Dihedral energy 0.06654 Other: 0.00000 Restraints energy 0.00025 Other: 0.00000 INTRNL energy 661.18325 Other: 661.03835 Comm force 4619.52978 Other: 0.00000 Energy time 5285.87593 Other: 0.00000 Total time 5299.46880 Other: 13.56281
NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 290712 STACK CURRENTLY IN USE IS 0 NO WARNINGS WERE ISSUED HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 0 MAXIMUM SPACE USED IS 5042840 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0
$$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 1.47 HOURS CPU TIME: 35.96 SECONDS * QM/MM Free Energy Perturbation Example: Water Dimer * bomlev -3 if ?qchem .ne. 1 then echo "cquantumtest/qmmm_pert.inp> Test NOT performed." stop endif
STREam datadir.def read rtf card * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19 * 20 1 ! Version number MASS 4 HT 1.00800 ! TIPS3P WATER HYDROGEN MASS 58 OT 15.99940 ! TIPS3P WATER OXYGEN RESI TIP3 .000 ! TIPS3P WATER MODEL GROUP ATOM OH2 OT -0.834 ATOM H1 HT 0.417 ATOM H2 HT 0.417 BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE ANGLE H1 OH2 H2 !ACCE OH2 IC H1 OH2 H2 BLN 0.0 0.0 0.0 0.0 0.0 IC H2 OH2 H1 BLN 0.0 0.0 0.0 0.0 0.0 PATC FIRS NONE LAST NONE end read param card * BOND HT OT 450.0 0.9572 ! from TIPS3P geometry HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) ANGLE HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY
NONBONDED NBXMOD 5 ATOM CDIEL SHIFT VATOM VDISTANCE VSHIFT - CUTNB 12.0 CTOFNB 10.5 CTONNB 9.0 EPS 1.0 E14FAC 0.4 WMIN 1.5 !
HT 0.0440 -0.0498 0.8000 !TIP3P water hydrogen, see NBFIX below OT 0.8400 -0.1591 1.6000 !TIP3P water oxygen, see NBFIX below
NBFIX ! Emin Rmin ! (kcal/mol) (A) ! ! We're gonna NBFIX the TIP3P water-water interactions ! here to make them more like Jorgensen's. The vdW parameters ! specified above will be in effect, therefore, for ONLY ! protein (read, protein OR nucleic acid)-water interactions. ! OT-OT is exactly Jorgensen's; HT interactions are added ! here. ! OT OT -0.152073 3.5365 ! TIPS3P VDW INTERACTION HT HT -0.04598 0.4490 HT OT -0.08363 1.9927 end
!------read sequence TIP3 2 gener W noangle nodihedral read coor card * QM/MM Pert Test Case: Water Dimer * DATE: 01/14/05 11:55:32 CREATED BY USER: hlwood * 6 1 1 TIP3 OH2 -1.30910 -0.25601 -0.24045 W 1 0.00000 2 1 TIP3 H1 -1.85344 0.07163 0.52275 W 1 0.00000 3 1 TIP3 H2 -1.70410 0.16529 -1.04499 W 1 0.00000 4 2 TIP3 OH2 1.37293 0.05498 0.10603 W 2 0.00000 5 2 TIP3 H1 1.65858 -0.85643 0.10318 W 2 0.00000 6 2 TIP3 H2 0.40780 -0.02508 -0.02820 W 2 0.00000
!------envi qchemexe "qchem" ! Command to call quantum program envi qchemcnt "data/qchem_pert.inp" ! Non Pert Control file envi qcheminp "q1.inp" ! Non Pert Quantum input file envi qchemout "qchem.out" ! Non Pert Quantum output file envi sainp "data/s0.inp" ! State 0 control file envi sbinp "data/s1.inp" ! State 1 control file envi stateainp "state0.inp" ! State 0 quantum input file envi statebinp "state1.inp" ! State 1 quantum input file envi stateaout "state0.out" ! State 0 quantum output file envi statebout "state1.out" ! State 1 quantum output file !------qchem remove sele resid 2 show end
! Compute unperturbed energy coor force comp print coor comp
! Call Pert and scale the charges of lambda 1 state pert sele resid 1 end scalar charge show scalar charge mult 0.25 sele resid 1 end scalar charge show
! Lambda 0 energy lambda 0.0 coor force comp print coor comp
! Lambda 1 energy lambda 1.0 coor force comp print coor comp
! Lambda 0.5 ! Energy should be 1/2 of State 0 and State 1 energy lambda 0.5 coor force comp print coor comp stop $comment standard non-pert QM input $end
$rem exchange hf basis sto-3g qm_mm true jobtype force symmetry off sym_ignore true print_input false $end
$molecule 0 1 $end
------
$comment comming from state 0 $end
$rem exchange hf basis sto-3g qm_mm true jobtype force symmetry off sym_ignore true print_input false $end
$molecule 0 1 $end
------
$comment comming from state 1 $end
$rem exchange hf basis sto-3g qm_mm true jobtype force symmetry off sym_ignore true print_input false $end
$molecule 0 1 $end 1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 33a2 February 15, 2006 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.4.20-28.9smp(i686)@n190.lobos.nih.go Created on 3/21/ 6 at 0:50:14 by user: hlwood
Maximum number of ATOMS: 240480, and RESidues: 80160 Current HEAP size: 10240000, and STACK size: 10000000
Processing passed argument "-p4wd" RDTITL> * QM/MM FREE ENERGY PERTURBATION EXAMPLE: WATER DIMER RDTITL> *
CHARMM>
CHARMM> bomlev -3
CHARMM>
CHARMM> if ?qchem .ne. 1 then RDCMND substituted energy or value "?QCHEM" to "1" Comparing "1" and "1". IF test evaluated as false. Skip to ELSE or ENDIF
CHARMM>
CHARMM> STREam datadir.def VOPEN> Attempting to open::datadir.def:: OPNLGU> Unit 99 opened for READONLY access to datadir.def
INPUT STREAM SWITCHING TO UNIT 99 RDTITL> * CHARMM TESTCASE DATA DIRECTORY ASSIGNMENT RDTITL> * Parameter: IN1 <- ""
CHARMM> faster on MISCOM> FAST option: EXPANDED (limited fast routines)
CHARMM> set 0 data/ ! input data directory Parameter: 0 <- "DATA/"
CHARMM> set 9 scratch/ ! scratch directory Parameter: 9 <- "SCRATCH/"
CHARMM> return VCLOSE: Closing unit 99 with status "KEEP"
RETURNING TO INPUT STREAM 5
CHARMM>
CHARMM> read rtf card MAINIO> Residue topology file being read from unit 5. RDTITL> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19 RDTITL> *
CHARMM>
CHARMM> read param card
PARAMETER FILE BEING READ FROM UNIT 5 RDTITL> * RDTITL> No title read. PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM>
CHARMM> !------CHARMM>
CHARMM> read sequence TIP3 2
CHARMM> gener W noangle nodihedral NO PATCHING WILL BE DONE ON THE FIRST RESIDUE NO PATCHING WILL BE DONE ON THE LAST RESIDUE GENPSF> Segment 1 has been generated. Its identifier is W. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 2 Number of atoms = 6 Number of groups = 2 Number of bonds = 6 Number of angles = 2 Number of dihedrals = 0 Number of impropers = 0 Number of cross-terms = 0 Number of HB acceptors = 0 Number of HB donors = 0 Number of NB exclusions = 0 Total charge = 0.00000
CHARMM>
CHARMM> read coor card SPATIAL COORDINATES BEING READ FROM UNIT 5 RDTITL> * QM/MM PERT TEST CASE: WATER DIMER RDTITL> * DATE: 01/14/05 11:55:32 CREATED BY USER: HLWOOD RDTITL> *
CHARMM>
CHARMM>
CHARMM> !------CHARMM> envi qchemexe "qchem" ! Command to call quantum program
CHARMM> envi qchemcnt "data/qchem_pert.inp" ! Non Pert Control file
CHARMM> envi qcheminp "q1.inp" ! Non Pert Quantum input file
CHARMM> envi qchemout "qchem.out" ! Non Pert Quantum output file
CHARMM> envi sainp "data/s0.inp" ! State 0 control file
CHARMM> envi sbinp "data/s1.inp" ! State 1 control file
CHARMM> envi stateainp "state0.inp" ! State 0 quantum input file
CHARMM> envi statebinp "state1.inp" ! State 1 quantum input file
CHARMM> envi stateaout "state0.out" ! State 0 quantum output file
CHARMM> envi statebout "state1.out" ! State 1 quantum output file
CHARMM> !------CHARMM>
CHARMM> qchem remove sele resid 2 show end The following atoms are currently set: SEGId RESId RESName .. TYPEs .. W 2 TIP3 OH2 H1 H2 SELRPN> 3 atoms have been selected out of 6 QCHEM> REMOve: Classical energies within QM atoms are removed. QCHEM> No EXGRoup: QM/MM Elec. for link atom host only is removed. QCHEM> No QINP: Charges will be based on atomic numbers. ------QCHEM: Classical atoms excluded from the QM calculation: NONE. QCHEM: Quantum mechanical atoms: 4 W 2 TIP3 OH2 5 W 2 TIP3 H1 6 W 2 TIP3 H2 QCHEM: Quantum mechanical link atoms: NONE. ------
CHARMM>
CHARMM> ! Compute unperturbed CHARMM> energy
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSHIft BYGRoup NOEXtnd NOEWald CUTNB = 12.000 CTEXNB =999.000 CTONNB = 9.000 CTOFNB = 10.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 0.400 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions.
General atom nonbond list generation found: 9 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
QCHEM> QCHEM> Q-Chem Job Parameters QCHEM> ------QCHEM> exchange hf QCHEM> basis sto-3g QCHEM> FINDEL: Quantum atom 4 W 2 TIP3 OH2 assigned to element: O 8 FINDEL: Quantum atom 5 W 2 TIP3 H1 assigned to element: H 1 FINDEL: Quantum atom 6 W 2 TIP3 H2 assigned to element: H 1 ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ENER QUANTUM: QMELec QMVDw ------ENER> 0 -47044.41961 0.00000 22.67055 ENER INTERN> 1.07269 0.01264 0.00000 0.00000 0.00000 ENER EXTERN> 2.06484 0.00000 0.00000 0.00000 0.00000 ENER QUANTM> -47047.56978 0.00000 ------
CHARMM>
CHARMM> coor force comp SELECTED FORCES COPIED TO THE COMPARISON SET.
CHARMM> print coor comp
COORDINATE FILE MODULE TITLE> * QM/MM FREE ENERGY PERTURBATION EXAMPLE: WATER DIMER TITLE> * 6 1 1 TIP3 OH2 25.62381 -19.44381 -0.59995 W 1 0.00000 2 1 TIP3 H1 -13.79853 8.64411 24.56699 W 1 0.00000 3 1 TIP3 H2 -8.17716 10.67749 -23.53745 W 1 0.00000 4 2 TIP3 OH2 -11.50628 -58.93639 -4.17580 W 2 0.00000 5 2 TIP3 H1 -8.81545 50.52325 1.13058 W 2 0.00000 6 2 TIP3 H2 16.67362 8.53535 2.61562 W 2 0.00000
CHARMM>
CHARMM> ! Call Pert and scale the charges of lambda 1 state CHARMM> pert sele resid 1 end VEHEAP> Expanding heap size by 5701632 words. SELRPN> 3 atoms have been selected out of 6 PERT: The current PSF is saved as lambda=0 for subsequent calculations. PERT: Number of atoms treated as changing: 3
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSHIft BYGRoup NOEXtnd NOEWald CUTNB = 12.000 CTEXNB =999.000 CTONNB = 9.000 CTOFNB = 10.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 0.400 EPS = 1.000 NBXMOD = 5 There are 9 atom pairs and 6 atom exclusions. There are 0 group pairs and 0 group exclusions.
CHARMM> scalar charge show ( W TIP3 1 OH2 ) -0.83400 ( W TIP3 1 H1 ) 0.41700 ( W TIP3 1 H2 ) 0.41700 ( W TIP3 2 OH2 ) 0.0000 ( W TIP3 2 H1 ) 0.0000 ( W TIP3 2 H2 ) 0.0000
CHARMM> scalar charge mult 0.25 sele resid 1 end SELRPN> 3 atoms have been selected out of 6
CHARMM> scalar charge show ( W TIP3 1 OH2 ) -0.20850 ( W TIP3 1 H1 ) 0.10425 ( W TIP3 1 H2 ) 0.10425 ( W TIP3 2 OH2 ) 0.0000 ( W TIP3 2 H1 ) 0.0000 ( W TIP3 2 H2 ) 0.0000
CHARMM>
CHARMM> ! Lambda 0 CHARMM> energy lambda 0.0
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSHIft BYGRoup NOEXtnd NOEWald CUTNB = 12.000 CTEXNB =999.000 CTONNB = 9.000 CTOFNB = 10.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 0.400 EPS = 1.000 NBXMOD = 5 There are 9 atom pairs and 6 atom exclusions. There are 0 group pairs and 0 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13 ATOM PAIRS AND 0 GROUP PAIRS SPACE FOR 13 REACTANT ATOM PAIRS, AND 0 GROUP PAIRS. SPACE FOR 13 PRODUCT ATOM PAIRS, AND 0 GROUP PAIRS.
General atom nonbond list generation found: 0 ATOM PAIRS WERE FOUND FOR ATOM LIST 9 ATOM PAIRS WERE FOUND FOR REACTANT LIST 9 ATOM PAIRS WERE FOUND FOR PRODUCT LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
PERTURBATION> Free energy perturbation calculation initiated. PERTURBATION> PSTART= 0 PSTOP= 0 PERTURBATION> LSTART= 0.000000 LSTOP= 0.000000 LAMBDA= 0.000000 PERTURBATION> Windowing will be used. PERTURBATION> TOTALS since last reset: PTOT> 0 0.00000 0.00000 0.00000 0.00000 0.00000 PTOT PROP> 0.00000 0.00000 0.00000 0.00000 0.00000 PTOT PRESS> 0.00000 0.00000 0.00000 0.00000 0.00000 ------PERTURBATION> Auto mode ends: PERT run terminated. ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ENER QUANTUM: QMELec QMVDw ------ENER> 0 -47044.41961 0.00000 22.67055 ENER INTERN> 1.07269 0.01264 0.00000 0.00000 0.00000 ENER EXTERN> 2.06484 0.00000 0.00000 0.00000 0.00000 ENER QUANTM> -47047.56978 0.00000 ------PERTURBATION> TOTALS since last reset: PTOT> 0 0.00000 0.00000 0.00000 0.00000 0.00000 PTOT PROP> 0.00000 0.00000 0.00000 0.00000 0.00000 PTOT PRESS> 0.00000 0.00000 0.00000 0.00000 0.00000 ------
CHARMM> coor force comp SELECTED FORCES COPIED TO THE COMPARISON SET.
CHARMM> print coor comp
COORDINATE FILE MODULE TITLE> * QM/MM FREE ENERGY PERTURBATION EXAMPLE: WATER DIMER TITLE> * 6 1 1 TIP3 OH2 25.62381 -19.44381 -0.59995 W 1 0.00000 2 1 TIP3 H1 -13.79853 8.64411 24.56699 W 1 0.00000 3 1 TIP3 H2 -8.17716 10.67749 -23.53745 W 1 0.00000 4 2 TIP3 OH2 -11.50628 -58.93639 -4.17580 W 2 0.00000 5 2 TIP3 H1 -8.81545 50.52325 1.13058 W 2 0.00000 6 2 TIP3 H2 16.67362 8.53535 2.61562 W 2 0.00000
CHARMM>
CHARMM> ! Lambda 1 CHARMM> energy lambda 1.0
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSHIft BYGRoup NOEXtnd NOEWald CUTNB = 12.000 CTEXNB =999.000 CTONNB = 9.000 CTOFNB = 10.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 0.400 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 6 atom exclusions. There are 0 group pairs and 0 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13 ATOM PAIRS AND 0 GROUP PAIRS SPACE FOR 13 REACTANT ATOM PAIRS, AND 0 GROUP PAIRS. SPACE FOR 13 PRODUCT ATOM PAIRS, AND 0 GROUP PAIRS.
General atom nonbond list generation found: 0 ATOM PAIRS WERE FOUND FOR ATOM LIST 9 ATOM PAIRS WERE FOUND FOR REACTANT LIST 9 ATOM PAIRS WERE FOUND FOR PRODUCT LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
PERTPS> ::WARNING:: LAMBDA value of 1.000000 is not between LSTART and LSTOP 0.000000 0.000000
***** LEVEL -2 WARNING FROM
PERTURBATION> Free energy perturbation calculation initiated. PERTURBATION> PSTART= 0 PSTOP= 0 PERTURBATION> LSTART= 0.000000 LSTOP= 0.000000 LAMBDA= 1.000000 PERTURBATION> Windowing will be used. PERTURBATION> TOTALS since last reset: PTOT> 0 0.00000 0.00000 0.00000 0.00000 0.00000 PTOT PROP> 0.00000 0.00000 0.00000 0.00000 0.00000 PTOT PRESS> 0.00000 0.00000 0.00000 0.00000 0.00000 ------PERTURBATION> Auto mode ends: PERT run terminated. ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ENER QUANTUM: QMELec QMVDw ------ENER> 0 -47039.20769 -5.21192 24.03488 ENER INTERN> 1.07269 0.01264 0.00000 0.00000 0.00000 ENER EXTERN> 2.06484 0.00000 0.00000 0.00000 0.00000 ENER QUANTM> -47042.35786 0.00000 ------PERTURBATION> TOTALS since last reset: PTOT> 0 0.00000 0.00000 0.00000 0.00000 0.00000 PTOT PROP> 0.00000 0.00000 0.00000 0.00000 0.00000 PTOT PRESS> 0.00000 0.00000 0.00000 0.00000 0.00000 ------
CHARMM> coor force comp SELECTED FORCES COPIED TO THE COMPARISON SET.
CHARMM> print coor comp
COORDINATE FILE MODULE TITLE> * QM/MM FREE ENERGY PERTURBATION EXAMPLE: WATER DIMER TITLE> * 6 1 1 TIP3 OH2 37.62939 -19.82670 0.72815 W 1 0.00000 2 1 TIP3 H1 -16.10554 9.47575 25.56515 W 1 0.00000 3 1 TIP3 H2 -10.20805 11.61802 -24.84401 W 1 0.00000 4 2 TIP3 OH2 -13.74036 -59.84492 -4.46451 W 2 0.00000 5 2 TIP3 H1 -9.58370 51.45383 1.05185 W 2 0.00000 6 2 TIP3 H2 12.00826 7.12402 1.96337 W 2 0.00000
CHARMM>
CHARMM> ! Lambda 0.5 CHARMM> ! Energy should be 1/2 of State 0 and State 1 CHARMM> energy lambda 0.5
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSHIft BYGRoup NOEXtnd NOEWald CUTNB = 12.000 CTEXNB =999.000 CTONNB = 9.000 CTOFNB = 10.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 0.400 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 6 atom exclusions. There are 0 group pairs and 0 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13 ATOM PAIRS AND 0 GROUP PAIRS SPACE FOR 13 REACTANT ATOM PAIRS, AND 0 GROUP PAIRS. SPACE FOR 13 PRODUCT ATOM PAIRS, AND 0 GROUP PAIRS.
General atom nonbond list generation found: 0 ATOM PAIRS WERE FOUND FOR ATOM LIST 9 ATOM PAIRS WERE FOUND FOR REACTANT LIST 9 ATOM PAIRS WERE FOUND FOR PRODUCT LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES PERTPS> ::WARNING:: LAMBDA value of 0.500000 is not between LSTART and LSTOP 0.000000 0.000000
***** LEVEL -2 WARNING FROM
PERTURBATION> Free energy perturbation calculation initiated. PERTURBATION> PSTART= 0 PSTOP= 0 PERTURBATION> LSTART= 0.000000 LSTOP= 0.000000 LAMBDA= 0.500000 PERTURBATION> Windowing will be used. PERTURBATION> TOTALS since last reset: PTOT> 0 0.00000 0.00000 0.00000 0.00000 0.00000 PTOT PROP> 0.00000 0.00000 0.00000 0.00000 0.00000 PTOT PRESS> 0.00000 0.00000 0.00000 0.00000 0.00000 ------PERTURBATION> Auto mode ends: PERT run terminated. ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ENER QUANTUM: QMELec QMVDw ------ENER> 0 -47041.81365 2.60596 23.30574 ENER INTERN> 1.07269 0.01264 0.00000 0.00000 0.00000 ENER EXTERN> 2.06484 0.00000 0.00000 0.00000 0.00000 ENER QUANTM> -47044.96382 0.00000 ------PERTURBATION> TOTALS since last reset: PTOT> 0 0.00000 0.00000 0.00000 0.00000 0.00000 PTOT PROP> 0.00000 0.00000 0.00000 0.00000 0.00000 PTOT PRESS> 0.00000 0.00000 0.00000 0.00000 0.00000 ------
CHARMM> coor force comp SELECTED FORCES COPIED TO THE COMPARISON SET.
CHARMM> print coor comp
COORDINATE FILE MODULE TITLE> * QM/MM FREE ENERGY PERTURBATION EXAMPLE: WATER DIMER TITLE> * 6 1 1 TIP3 OH2 31.62660 -19.63525 0.06410 W 1 0.00000 2 1 TIP3 H1 -14.95204 9.05993 25.06607 W 1 0.00000 3 1 TIP3 H2 -9.19260 11.14775 -24.19073 W 1 0.00000 4 2 TIP3 OH2 -12.62332 -59.39065 -4.32015 W 2 0.00000 5 2 TIP3 H1 -9.19958 50.98854 1.09122 W 2 0.00000 6 2 TIP3 H2 14.34094 7.82969 2.28950 W 2 0.00000
CHARMM>
CHARMM> stop Parallel load balance (sec.): Node Eext Eint Wait Comm List Integ Total 0 15.2 18.1 0.0 0.0 0.0 0.0 33.3
$$$$$$ New timer profile Local node$$$$$ List time 0.00121 Other: 0.00000 Electrostatic & VDW 0.00010 Other: 0.00000 Nonbond force 0.00010 Other: 0.00000 Bond energy 0.00002 Other: 0.00000 Angle energy 0.00001 Other: 0.00000 Dihedral energy 0.00001 Other: 0.00000 Restraints energy 0.00001 Other: 0.00000 INTRNL energy 18.09905 Other: 18.09901 Comm force 0.00001 Other: 0.00000 Energy time 18.09916 Other: 0.00000 Total time 18.18032 Other: 0.07994
$$$$$$ Average profile $$$$$
List time 0.00121 Other: 0.00000 Electrostatic & VDW 0.00010 Other: 0.00000 Nonbond force 0.00010 Other: 0.00000 Bond energy 0.00002 Other: 0.00000 Angle energy 0.00001 Other: 0.00000 Dihedral energy 0.00001 Other: 0.00000 Restraints energy 0.00001 Other: 0.00000 INTRNL energy 18.09905 Other: 18.09901 Comm force 0.00001 Other: 0.00000 Energy time 18.09916 Other: 0.00000 Total time 18.18032 Other: 0.07994
NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 80160 STACK CURRENTLY IN USE IS 0 MOST SEVERE WARNING WAS AT LEVEL -2 HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 13006152 MAXIMUM SPACE USED IS 13008060 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 2924254 NEXT: 10238857 PRINHP> ADDRESS: 10238857 LENGTH: 980 NEXT: 10239937 PRINHP> ADDRESS: 10239937 LENGTH: 64 NEXT: 159782881 PRINHP> ADDRESS: 159782881 LENGTH: 10182 NEXT: 0
$$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 18.18 SECONDS CPU TIME: 0.09 SECONDS