[gmx-users] Fatal Equilibration Errors

Bruce D. Ray brucedray at yahoo.com
Thu Aug 13 13:42:57 CEST 2009

On Wednesday, August 12, 2009 at 8:47:33 PM, Nancy <nancy5villa at gmail.com> wrote:

> In an earlier message, it was stated that topolbuild generated
topologies with Gromos 53a6
> and OPLS-AA force fields.  I am using
topolbuild (version 1.2.2), and the only files in the
> "dat/gromacs"
directory are for the force fields: 43a1, 43a2, 43b1, 45a3, 53a5, and
> How is the OPLS-AA force field used?

First, I need to thank you in particular.  First, while testing your molecules, I discovered a
case in the as yet unreleased topolbuild 1.3 in which my dihedral selection method failed
to select the dihedral choice with the maximum number of heavy atoms with OPLS-AA as
the force field. Second, also because of this, I discovered what one downloads as a "Sybyl
2" structure from one source of small molecule structures and how to edit it so that it meets
the syntax standards for a true mol2 file. Thank you very much for this assistance.

In the earlier message, I stated that topolbuild 1.2.1 ( and 1.2.2) generates topologies for
amber, gaff, glycam, 43a1, 43a2, 43b1, 45a3, 53a5, and
53a6.  I stated that the as yet
unreleased topolbuild 1.3 will include OPLS-AA. The version of topolbuild you have,
is 1.2.2. Would you like to beta test topolbuild 1.3?


Bruce D. Ray, Ph.D.
Associate Scientist
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273

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