[gmx-users] Fatal Equilibration Errors

[Nancy]

I'm glad to be of help; yes, I would like to beta test topolbuild 1.3.

Thank you.




On Thu, Aug 13, 2009 at 7:42 AM, Bruce D. Ray <brucedray at yahoo.com> wrote:

> 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 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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