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Macromodel Faqs MacroModel FAQs 1. What is the MacroModel product suite and how will it help my research? 2. What is the structure of MacroModel? 3. What is Maestro? 4. What is the latest version of MacroModel? 5. Under what hardware platforms and operating systems can current version of MacroModel be used? 6. Can I use a Macintosh or Windows PC as a display for MacroModel? 7. What structure file formats can be used with the MacroModel package? 8. How do I find information about atomic charges used in MacroModel calculations? 9. MacroModel contains a variety of force fields. Which is best for my purpose? 10. How can I tell what force field parameters were used in a particular simulation? 11. I need to add parameters to MacroModel. How is this done? 12. When performing a conformational search, how do I judge whether the search has covered the complete conformation space? 13. How do I set up Jumping Between Wells (JBW) or Free Energy Perturbation (FEP) computa- tions with MacroModel? 14. What is XCluster and how can it help me in my research? MacroModel FAQs What is the MacroModel product suite and how will it help my research? MacroModel is a premier molecular mechanics and modeling software package that consists of the Maestro graphical user interface, the BatchMin molecular mechanical computational engine, and the XCluster and MINTA analysis modules. The Maestro interface provides easy-to-use tools for building and manipulating both simple and complex chemical structures, and the BatchMin computational engine contains powerful algorithms for performing conformational searches and free energy simulations. In addition, BatchMin’s molecular mechanics and dynamics modeling techniques can be applied together to evaluate the energies and geometries of chemical systems in vacuum and in solution. Solution studies can be performed using MacroModel’s accurate and efficient GB/SA continuum solvation model. MacroModel is not designed to perform ab-initio quantum mechanical calculations or explicit solvent simulations using periodic boundary conditions. Additionally, no tools are included for chemical information handling (database management), pharmacophore generation, or QSAR analysis. For conducting sophisticated, high-performance quantum chemical calculations, we rec- ommend using Jaguar. For study of protein-drug interactions, we recommend using the innovative protein active-site modeling application QSite. [Back] MacroModel FAQs What is the structure of MacroModel? The MacroModel molecular modeling package is comprised of four programs: 1) The Maestro graphical user interface 2) The MacroModel energetic computational engine BatchMin 3) The XCluster statistical cluster-analysis program 4) The MINTA free energy calculation program (licensed separately) 1) The Maestro graphical user interface provides common access to all Schrodinger modeling technologies and is designed to allow a simple and efficient workflow. Maestro is available for all platforms supported for MacroModel, and is included in the price of MacroModel. All Macro- Model versions to date also contain the MacroModel graphical user interface. The MacroModel interface can be executed only on the IBM AIX and SGI IRIX platforms. Support for the original MacroModel interface will soon be discontinued because the more powerful, expanded function, easy-to-use Maestro interface is now available. 2) The MacroModel energetic computational engine is called BatchMin. BatchMin energy calcu- lations can be initiated from the MacroModel interface, from Maestro, or from the command line. 3) XCluster is a tool for observing, analyzing and visualizing the clustering of molecular confor- mations. 4) Minta directly calculates the relative free energy of molecular configurations. [Back] MacroModel FAQs What is Maestro? Maestro is a powerful, unified, multi-platform graphical user interface that can be used to build structures and to quickly and easily set up and submit energetic calculations to the Macro- Model, Impact, Glide, QSite, Liaison, and Jaguar computational engines. Maestro contains moni- toring and analysis features and a scripting ability that can be used to automate large or repetitive tasks. In addition, Maestro contains a wide range of useful display options, a comprehensive, user-extensible molecular builder that includes the ability to sketch structures or build them from fragments. See the Maestro Release Notes for a more detailed description of Maestro features. [Back] MacroModel FAQs What is the latest version of MacroModel? MacroModel 7.1 was released in January 2001. It includes version 3.0 of the Maestro graphi- cal interface, which can be run on all MacroModel-supported platforms. [Back] MacroModel FAQs Under what hardware platforms and operating systems can current version of MacroModel be used? MacroModel is supported on SGI IRIX 6.5.2m, IBM AIX 4.3.2.0, Compaq (DEC) Tru64 UNIX V4.0F, Hewlett-Packard HPUX 11.00, Sun SunOS 5.7 (Solaris 7), and Linux kernel 2.0.36 (Red Hat 5.2, Suse 6.2). Most OS versions later than the above are also supported. For more infor- mation, see the supported platforms page for MacroModel and Maestro. [Back] MacroModel FAQs Can I use a Macintosh or Windows PC as a display for MacroModel? The MacroModel interface can be run on any supported SGI or IBM machine and displayed, using the X-Windows system or an X-Windows emulator, over a network to another machine. However, X-emulation does not support all advanced rendering options which are available for the IBM and SGI IRIX GL versions of the MacroModel interface. Support for the MacroModel interface will soon be discontinued due to the development and release of Schrodinger’s new and advanced graphical interface Maestro. With the exception of the Linux version, Maestro is an OpenGL application. The Linux version will display to any X-server. The OpenGL Maestro ver- sions will display to any X-server that has the GLX and OpenGL extensions. Examples are Exceed/OpenGL, from Hummingbird, for the PC, and Exodus/OpenGL, from White Pine Soft- ware, for the Mac/PowerPC. [Back] MacroModel FAQs What structure file formats can be used with the MacroModel package? The Maestro interface for MacroModel has the ability to read and write files in the following formats: • MacroModel • Maestro • PDB • Sybyl Mol2 • MDL SD (.mol) The MacroModel installation also includes command line routines for interconversion between many of the above file types. [Back] MacroModel FAQs How do I find information about atomic charges used in MacroModel calculations? Usually, partial atomic charges used in an energetic computation are obtained from informa- tion stored in the force-field (.fld) file (or from the BMFF co-process, for OPLS-2000 or MMFF). However, BatchMin will use the charges that appear in the structure input file if the CHGF com- mand appears in the BatchMin command file. After an energetic computation is complete, the charges—as determined by the force field in use—appear in the output structure file. When the force-field file is used as the charge source, there are three types of information that affect the partial charges: bond dipoles, formal charges, and explicit substructure charges. Bond Dipoles Bond dipoles are stored in the stretch part of the force field. The following example is from the AMBER* force field: 1 CT - H1 1.0900 331.0000 -0.6597 N400 0000 ^^^^^^^ The indicated number is the bond dipole (D, in DeByes) that is applied between types CT and H1. Partial charges Q and -Q would be assigned to the atoms CT and H1 respectively based upon the relation: Q = 0.2082 * Dipole/ L0 where L0 is the “natural” bond length in Angstroms. The charge for atoms which have more than one bonded attachment is the sum of all the con- tributions from the bond dipoles. This method of charge accounting has the significant advantage that it is guaranteed to maintain charge neutrality. Formal Charges Some atom types (like OM: O-) have a “formal” charge which is added to the partial atomic charge calculated by the bond dipole method. Substructure Charges Finally, there are a few cases where atomic charges are stored directly in the substructure part of the force field. In general, however, we have attempted to avoid this and most charges come from bond dipoles. See Appendix 5 “The BMFF Protocol” in the BatchMin Reference Manual for further details. [Back] MacroModel FAQs MacroModel contains a variety of force fields. Which is best for my purpose? Each of the MacroModel force fields has strengths, but in general, the most complete and well parameterized force fields are MMFF and OPLS-2000. The other force fields are routinely used for special situations; for example, when using united atoms (AMBER*) or when reproducing or extending previous results. Although there are no absolute guidelines available for choosing the most appropriate MacroModel force field for a given molecular modeling application, the follow- ing generalizations are reasonable: OPLS-2000: Probably the best available force field for condensed-phase simulation of peptides. Work to develop parameterization that will include broader classes of drug- like molecules is ongoing. GB/SA solvation energies are good. MMFF: An excellent force field for biopolymers and many organic molecules that do not have parameters in other force fields. AMBER*/OPLS*: Good force fields for biopolymers and carbohydrates; we have added many parameters which extend the scope of this force field to a number of important organic functional groups. GB/SA solvation energies range from moderate (AMBER*) to good (OPLS*). AMBER94: An excellent force field for proteins and nucleic acids. However, there are no extensions for non-standard residues or organic molecules. MM2*/MM3*: Excellent force fields for hydrocarbons and molecules with single or remotely spaced functional groups. GB/SA solvation energies tend to be poor relative to those calculated with other force fields. Often when choosing a force field, you can use as a guide the parameter quality that is reported in the monitoring window of the interface and in the log file for the calculation.
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