[gmx-users] topolbuild 1.1.2, further revisions to an all-atoms model gromacs topology generator

Bruce D. Ray brucedray at yahoo.com
Fri Jul 11 21:20:13 CEST 2008

I have submitted a further revision of topolbuild as file
topolbuild1_1_2.tgz that has the ability to use the new
antechamber tables included with AmberTools 1.0.

This version incorporates the following changes:
1. Changed maximum atom types allowed to permit use of the new version
   of ATOMTYPE_GFF.DEF distributed with AmberTools 1.0.
2. Improved determination of improper dihedrals.
3. Corrected atom type determination to set and to check for plain type
   AB bonds.
4. Made cosmetic corrections to log file output.
5. Included a gaff.dat file modified from the one distributed with
   AmberTools 1.0 to add atom type cz entries for mass and polarizability,
   for improper dihedrals, and for van Der Waals interactions.
6. Replaced the ATOMTYPE_GFF.DEF file with one derived from the
   ATOMTYPE_GFF.DEF distributed with AmberTools 1.0.

Once again, 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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