[gmx-users] topolbuild: attempt at a Gromacs topology builder added to Gromacs user contributed software

Bruce Ray brucedray at yahoo.com
Mon Aug 20 15:01:34 CEST 2007

I got frustrated with the options for building
topologies for ligands and wrote this to allow me to
use bond length and angle values derived from prior
modeling and NMR data.
There probably will be something better than this from
the developers at some point, but I decided to upload
what I have to Gromacs contributed software.

To build a gaff or amber## based topology, the builder
requires the antechamber atom type definition files
and the gaff and amber## parm files as found in the
dat directory for antechamber-1.27 (files in
directories dat/antechamber and dat/leap/parm).  To
build a Tripos force field based topology, the builder
requires the TAFF* files found in the Tripos directory
pointed to by the Tripos variable $TA_ASCTABLES .  The
builder has options to renumber atoms and residues to
decrease the editing required to add a ligand to a
system, to revise atom naming for consistency (only
useful with small molecule ligands), and to use bond
lengths and angle values derived from coordinates
instead of set by the force field.  The builder also
converts Tripos distance restraints to Gromacs
distance restraints.  (As noted in the NOT_DONE file
in the submission, there seem to be some differences
between what Tripos gives as an angle restraint and
what Gromacs wants as an angle restraint.) 

The file is topolbuild.tgz and includes a text file
describing the testing I've done so far of topologies
built with this program (PROGRAM_TESTING_DONE) along
with other descriptive material including indications
of possibilities for expansion to other all atom
force fields.  As noted above, the NOT_DONE file
indicates things this contribution does not include.
INVENTORY is a list of all files in the contribution.
PROGRAM_UNITS lists the program files in the
contribution and the purposes they serves, and lists
seperately the header files and the program files
that call for them.  The README should be enough for
installation and usage documentation.

Note that the antechamber and Tripos force field files
are not included in the contribution.  These will have
to be placed in appropriate directories separately.
This contribution does, however, include water and
ions force field files suitable for use with gaff.

I hope this proves useful to somebody.


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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