[gmx-users] Topology from semiempiricaly optimized structure

[Semen Esilevsky]

You see, I've tried PRODRG and it does not work for
me. It disrupts the geometry I supply even if I don't
ask for energy minimization. I'm not sure if it is a
bug, but this server doesn't help much.

--- Daan van Aalten <vdava at davapc1.bioch.dundee.ac.uk>
wrote:
> 
> if you are happy with sticking with the ffgmx force
> field, the PRODRG
> server will give you a topology for your molecule,
> see
> http://davapc1.bioch.dundee.ac.uk/prodrg
> 
> Daan
> 
> On Fri, 11 Jun 2004, Semen Esilevsky wrote:
> 
> > Hi all!
> > I have a small molecule (a fluorescent probe),
> which
> > is optimized on the semiempirical level, so I know
> the
> > geometry. As far as I understand the only way to
> make
> > a topology for it is to write it by hands using
> > appropriate atom types and forcefield parameters.
> > However it seems to be a week of work for ~80
> atoms.
> > Does the program (or script) exists for this
> routine
> > task?
> >
> > Thank you in advance,
> > Semen
> >
> >
> >
> >
> >
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> 
>
##############################################################################
> Dr. Daan van Aalten                    Wellcome
> Trust Senior Fellow / Reader
> Wellcome Trust Biocentre, Dow Street   TEL: ++ 44
> 1382 344979
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