[gmx-users] Topology from semiempiricaly optimized structure

[Daan van Aalten]

Hi Semen

Would it be possible for you to send us the input coordinates so we can
see what goes wrong? Do I correctly interpret your E-mail to say that the
coordinates are screwed up even if you minimize on the server?

cheers

Daan

On Sat, 12 Jun 2004, Semen Esilevsky wrote:

> 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
> > Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44
> > 1382 345764
> > School of Life Sciences                E-mail: see
> > WWW page
> > Univ. of Dundee, Dundee DD1 5EH, UK    WWW:
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> >
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##############################################################################
Dr. Daan van Aalten                    Wellcome Trust Senior Fellow / Reader
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: see WWW page
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk