Bruce, This is great. I was able to easily make a molecule that runs with OPLS-AA. Would it be possible to add a feature which creates an *.rtp entry? It would be really useful for making non standard amino acids and incorporating it with pdb2gmx.
Thanks, Ilya On Wed, Mar 10, 2010 at 11:07 AM, Bruce D. Ray <[email protected]> wrote: > I have uploaded to the user contributed software at gromacs.org a > further revision of topolbuild that includes support for OPLS-AA as > file topolbuild1_3.tgz > > topolbuild 1.3 > Reads a syntactically correct Tripos .mol2 file with charges to generate > something approximating gromacs *.gro, *.top, and *.itp files from it > based on selected force field parameters. This version adds support for > oplsaa. Includes tables to support amber, gaff, glycam, oplsaa, and gmx > type force fields. Requires that the *.mol2 file have syntactically correct > Tripos atom types and absolutely will not work with other input atom > types. Includes capability of pruning dihedral angles to a possibly more > reasonable set. Note that the standard for a syntactically correct mol2 > file is the Tripos Toolkit Utilities Manual. > > Revisions include: > 1. Added OPLS-AA support, atom definition files, and force field > data tables. Best results for pruning of dihedral angles will > probably be with -purge 0 > 2. Corrected errors in setting some categories of rings > 3. Corrected Makefile to be compatible with more variants of make > 4. Increased initial estimate of maximum number of rings for ring > detection > 5. Added lines to log, topology, and include files to give version > and command line of invocation > 6. Made internal rearrangements to ease addition of and handling > of other force fields > 7. Set default prune of excess dihedral angles equivalent to -purge 1 > 8. Added option to translate molecule coordinates to center of > mass when renumbering is not requested > 9. Added elements to internal atomic masses / numbers table > 10. Revised method of correction of Tripos out of plane pyramid > height improper force constants to cosine function force constants > 11. Altered setting of dihedral phases for Tripos force field > 12. Changed error messages in mol2 file reading to give clearer > statement of problems > 13. Changed error for not ending the bonds section of the mol2 file > with @<TRIPOS> from fatal error to warning because mol2 files > supplied by some databases lack correct termination > 14. Added atom type default entries to the amber atom type definition > tables > 15. Corrected errors in gromacs topology defaults line settings. > 16. Changed preferences in dihedral angles purge to choose the > maximum number of heavy atoms possible for dihedrals retained > for topology output. > 17. Modified renaming. > 18. Use of distances and angles measured from structure no > longer affects dihedral values. > 19. Added -charge option to permit assignment of atom charges > based on atom type charges from force field. Currently only > OPLS-AA tables support this option. > > Special Processing Used for oplsaa Force Fields > With the exception of van der Waals parameters and default atom > charges, oplsaa is designed such that force field parameters are > associated with atom types from a modified and amplified version > of the Kollman atom types. However, oplsaa also uses a much richer > set of atom types to determine van der Waals parameters and default > atom charges. Therefore, generation of an oplsaa topology requires > double determination of atom types. A first determination of atom > types is performed with the expanded version of the Kollman atom > types. This assignment is used to assign force constants, bond lengths, > angles, dihedral angles, and improper angles. A second determination > of atom types is performed to assign final oplsaa atom types to match > the atom types in ffoplsaanb.itp from the gromacs distribution. A > major problem of this double conversion is that topolbuild does not > always select the exact same atom type for a residue listed in > ffoplsaa.rtp. The following table gives some of the differences > discovered: > residue atom rtp value topolbuild usage > HISA ND1 opls_503 opls_557 imidazole N1 > HISA HD1 opls_504 opls_562 imidazole H1 > HISA HE1 opls_146 opls_563 imidazole H2 > HISB HD2 opls_146 opls_565 imidazole H5 > HISB HE1 opls_146 opls_563 imidazole H2 > HISB NE2 opls_503 opls_557 imidazole N1 > HISB HE2 opls_504 opls_562 imidazole H1 > TRP HD1 opls_146 opls_597 indole H2 > TRP CE3 opls_145 opls_590 indole C4 > TRP HE3 opls_146 opls_599 indole H4 > TRP CZ2 opls_145 opls_593 indole C7 > TRP HZ2 opls_146 opls_602 indole H7 > TRP CZ3 opls_145 opls_591 indole C5 > TRP HZ3 opls_146 opls_600 indole H5 > TRP CH2 opls_145 opls_592 indole C6 > TRP HH2 opls_146 opls_601 indole H6 > > Because of the manner in which oplsaa constants were developed > originally, in all of these cases the same bond, angle, dihedral, and > improper constants are assigned. The van der Waals parameters are identical > between the original rtp atom type and the topolbuild choice > as well. When charges from the mol2 file rather than the oplsaa atom > type charges are used, differences in atom type charges are moot. > Thus, the effects of these changes are minimal. Curiously, the oplsaa > atom type charges from the topolbuild atom type selections appear > to be closer to the atom charges given in foplsaa.rtp than the atom > type charges for the oplsaa types used in foplsaa.rtp > > > I hope people find this version useful. > > > Sincerely, > > > -- > Bruce D. Ray, Ph.D. > Associate Scientist > IUPUI > Physics Dept. > 402 N. Blackford St. > Indianapolis, IN 46202-3273 > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. 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