MANUAL FOR THE MOLECULAR DYNAMICS PACKAGE Q version 4.20 Revised August 22, 2000 John Marelius Karin Kolmodin Ellen Kindlund Johan Åqvist* <[email protected]> Dept. of Cell and Molecular Biology Uppsala University, Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN Q web site:site: http://aqvist.bmc.uu.se/Q 1 Contents A. Introduction.............................................................................................................................................. 4 B. User guide ................................................................................................................................................ 5 B.1. Preparing a molecular topology.......................................................................................................... 6 B.1.1. Preparing coordinates................................................................................................................ 6 B.1.2. Selecting a force field................................................................................................................ 7 B.1.3. Adding force field library entries............................................................................................... 7 B.1.4. Running Qprep ......................................................................................................................... 7 B.2. Running dynamics with Qdyn ......................................................................................................... 10 B.2.1. Simulation procedure .............................................................................................................. 10 B.2.2. Output generated by Qdyn....................................................................................................... 11 B.2.3. Preparing Qdyn input files ...................................................................................................... 11 B.2.4. Qdyn input file examples......................................................................................................... 14 B.2.5. FEP file .................................................................................................................................. 16 B.2.6. Monitoring non-bonded interactions ........................................................................................ 21 B.3. Analysis of results........................................................................................................................... 22 B.3.1. Analysing structures from the simulation................................................................................. 22 B.3.2. Free energy calculation using Qfep.......................................................................................... 23 B.3.3. Reaction free energy averaging using avefep............................................................................ 25 B.3.4. Simple energy averaging using Qave........................................................................................ 26 B.3.5. Trajectory averaging using Qavetr............................................................................................ 26 B.4. Useful tips ...................................................................................................................................... 26 C. Tutorials ................................................................................................................................................. 27 C.1. Binding affinity of the FABP-stearate complex from LIE simulations ............................................... 27 C.1.1. Editing the PDB file................................................................................................................ 27 C.1.2. Modelling ionic groups of the protein....................................................................................... 27 C.1.3. Writing the library file ............................................................................................................ 28 C.1.4. Qprep...................................................................................................................................... 28 C.1.5. FEP files................................................................................................................................. 29 C.1.6. Creating input files.................................................................................................................. 29 C.1.7. Using Qdyn3........................................................................................................................... 29 C.1.8. Evaluating the simulation........................................................................................................ 29 D. Reference guide ..................................................................................................................................... 31 D.1. Force field reference information .................................................................................................... 31 D.2. Topology preparation reference ....................................................................................................... 33 D.2.1. Coordinate files for input into Qprep ....................................................................................... 33 D.2.2. Atom masks ............................................................................................................................ 34 D.2.3. Qprep commands .................................................................................................................... 35 D.2.4. Qprep preferences................................................................................................................... 36 D.2.5. Fragment library file format..................................................................................................... 36 D.2.6. Force field parameter file format ............................................................................................. 39 D.2.7. Solvent file format................................................................................................................... 43 D.3. Boundary conditions ....................................................................................................................... 43 D.3.1. Solute boundary restraints....................................................................................................... 43 D.3.2. Water boundary restraints ....................................................................................................... 44 D.4. Units .............................................................................................................................................. 45 D.5. File and format descriptions............................................................................................................ 45 D.5.1. Qdyn input file format............................................................................................................. 45 D.5.2. FEP file format ....................................................................................................................... 49 D.6. Log files.......................................................................................................................................... 55 D.6.1. Qdyn log file ........................................................................................................................... 55 D.6.2. Qfep log file............................................................................................................................ 59 D.7. Differences from earlier versions..................................................................................................... 59 D.7.1. Differences in Qprep............................................................................................................... 59 2 D.7.2. Differences in Qdyn ................................................................................................................ 60 D.8. Utility programs.............................................................................................................................. 60 D.8.1. proq - PDB file analysis and manipulation .............................................................................. 60 D.8.2. mdsh - input preparation shell ................................................................................................ 64 D.8.3. Analysis programs................................................................................................................... 67 D.8.4. Other utility programs ............................................................................................................. 68 E. System guide .......................................................................................................................................... 70 E.1. System requirements ....................................................................................................................... 70 E.1.1. Compilers................................................................................................................................ 70 E.2. Installation...................................................................................................................................... 70 E.2.1. Installing executable images.................................................................................................... 70 E.2.2. Building the programs from source code .................................................................................