[gmx-users] topolbuild 1.3, revision to topolbuild that incorporates OPLS-AA support

Joe Joe 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
with pdb2gmx.



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
>       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
> Physics Dept.
> 402 N. Blackford St.
> Indianapolis, IN 46202-3273
> --
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