[gmx-users] Topology from semiempiricaly optimized structure

[Daan van Aalten]

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: http://davapc1.bioch.dundee.ac.uk