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

Bruce D. Ray brucedray at yahoo.com
Wed Mar 10 20:07:52 CET 2010

I have uploaded to the user contributed software atgromacs.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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