[gmx-users] topolbuild 1.1.1, minor revisions to an all-atoms model gromacs topology generator

[Bruce D. Ray]

I have submitted a minor revision of topolbuild that
I hope is more portable.   Version 1.1.1 is now
available in the user contributions at the gromacs
web site.

The following revisions have been made:
 1. Removed all non-pointer references to NULL.
 2. Gave all external variables single defining
    declarations with initializations all set in the
    file initializations.c
 3. Corrected problem with carbonyls and some
    nitrogens when correcting for charges in atom type
    assignment.
 4. Altered atom ordering to put H's with their parent
    atoms.
 5. Added parameterization for the C -CT-NT angle in
    amber99 force field.  This parameterization is
    missing in amber99 and presumably in other
    editions of the amber force fields as well.
    Curiously, the equivalent parameterization is
    present in gaff.
 6. Divided force field output routines to better
    allow for addition of other force field output
    requirements.
 7. Added an attempt at dihedral restraints output in
    the topology.
 8. Changed the defines required for restraints.
 9. Arranged for all output to go to the current
    directory when the input .mol2 file is in another
    directory.  The parameter to the -n includes a
    directory path in such cases and the path is
    stripped from the names of the output files.

As with the original, the required input is a
syntactically correct mol2 file with Tripos atom
types.  At this time, output is still limited to
topologies with amber, gaff, or Tripos force fields.

I hope this proves useful.


Sincerely,





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


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