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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