[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
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.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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