[gmx-users] topolbuild 1.3, revision to topolbuild that incorporates OPLS-AA support
ilchorny at gmail.com
Wed Mar 10 21:35:38 CET 2010
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
On Wed, Mar 10, 2010 at 11:07 AM, Bruce D. Ray <brucedray at yahoo.com> 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
> 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
> 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
> 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.
> Bruce D. Ray, Ph.D.
> Associate Scientist
> Physics Dept.
> 402 N. Blackford St.
> Indianapolis, IN 46202-3273
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