[gmx-users] topolbuild 1.2.1, gromacs topology builder for gromacs and amber force field topologies

Bruce D. Ray brucedray at yahoo.com
Thu Dec 11 20:32:59 CET 2008

I have submitted a further revision of topolbuild as file topolbuild1_2_1.tgz
This should work much better than the previous release that was rushed
on account of personal factors that threatened to preclude further work.

topolbuild 1.2.1
Reads a Tripos .mol2 file with charges to generate something approximating gromacs *.gro, *.top, and *.itp files from it based on selected force field parameters.  Now supports some united atom force fields.  Includes tables to support amber, gaff, glycam, 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.

Revisions include:
  1.  Corrected errors in prior version from last minute additions.
  2.  Corrected output of defines and includes.
  3.  Refined the gromacs force field tables.
  4.  Revised log and topology outputs to better reflect the types of dihedrals.
  5.  Updated parameter files for gaff, glycam, and amber to the versions found in AmberTools 1.2
  6.  Revised order of setting dihedrals to better reflect tleap or grommp settings.
  7.  Improved option to prune excess dihedral angles.  Most users should be satisfied with the results from setting -purge 1
  8.  Improper dihedrals generated for amber, glycam, gaff, and Tripos force fields are now included with regular type 1 dihedrals in accordance with the way that amber treats improper dihedrals.
  9.  Ion type names for the amber force fields now written in the topology as atomic symbol with charge to differentiate from other atom types in some force fields.

Special Processing Used for Gromacs Force Fields
Gromacs force fields have a limited set of atom types that are used in multiple
chemical environments. This works quite well when one can use a residue types
file to generate a topology. This presents problems when the goal is to determine
the topology of an arbitrary molecule for which residue type information does not
exist. Therefore, conversion to gromacs force fields requires double determination
of atom types. A first determination of atom types is performed with a rich set
of atom types derived from a combination of the gaff and amber atom type
definitions. This assignment is used to determine force constants, bond lengths,
angles, dihedral angles, and improper angles. A second determination of atom
types is performed to assign the true gromacs atom types to match the atom
types in the appropriate ffG####nb.itp from the gromacs distribution. A major
problem of this double conversion is that for something found in a residue type
file, topolbuild does not always select the exact same parameters as are
found in the residue type file’s parameterization. However, tests so far give
the same parameterization better than 95% of the time.

As always, I hope people find this useful.


Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273


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