[gmx-users] Superpositioning small molecules

[aldo jongejan]

Many programs are available that can do superimposition. For example,

FIT
http://bioinfo1.mbfys.lu.se/~guoguang/fit.html

MOLMOL
http://www.mol.biol.ethz.ch/wuthrich/software/molmol

On the net, you might find many more...

aldo

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
>
> g_confrms can do that. It is part of the Gromacs package that you can
> get for free at www.gromacs.org. It only reads .pdb files, though (and
> some Gromacs specific formats).
>
> --
> 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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> |_____________|_______________________________________________________|
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--
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Aldo Jongejan
Molecular Modeling Group
Dept. of Pharmacochemistry
Free University of Amsterdam
De Boelelaan 1083
1081 HV Amsterdam
The Netherlands

e-mail: jongejan at chem.vu.nl
tlf:    +31 (0)20 4447612
fax:    +31 (0)20 4447610

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