On Wednesday, August 12, 2009 at 8:47:33 PM, Nancy <nancy5vi...@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
53a6.
> 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?
Sincerely,
--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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