[gmx-users] Superpositioning small molecules

[Daan van Aalten]

Hi Anton

PRODRG currently reads in MOL2 files and writes out the GMX .gro and .itp
files. Note that MOL2 files not only contain coordinate information, and
converting MOL2 *topology* information to GMX atomc types etc. or writing
it out is not trivial (I've spent the last 7 years optimising this in
PRODRG)

Daan

On Fri, 9 Jan 2004, Anton Feenstra wrote:

> dastmalchi.s at tbzmed.ac.ir wrote:
>
> > Hi,
> > Does any one know of the free program(s) to read in the small molecules,
> > preferably in mol2 of HIN formats, superimose them on the target molecule
> > (using the selected atoms) and write out the new coordinates of the
> > superimposed molecule in a file.
> > Cheers, Siavoush
>
> Talking about file formats, would people be interested in mol2 reading
> and/or writing capabilities in Gromacs?
>
>
> --
> Groetjes,
>
> Anton
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
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: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

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