[gmx-users] Topology utilities ?

[Daan van Aalten]

Hi Marc

Well actually the non-server version of PRODRG can do that (interactively
delete/remove hydrogens (POLAR ones, that is)) before writing out the
final topology. Similar for changing chirality.

Would it be useful to have that on the server as well?

cheers

Daan

On Wed, 13 Mar 2002, Marc Baaden wrote:

>
> Hi,
>
> I am struggling a bit with the setup of a ligand topology, for which
> I got a reasonable initial guess from Prodrg.
> But now I have to remove some hydrogens and things like that, as I
> need a charged state. So evrytime I remove a hydrogen, the topology
> file needs top be renumbered ..
> .. is there any tool (perl/C/Fortran or whatever script) around to
> do that ?
> Are any other useful topology handling tools available (like for putting
> in charges, ..) ?
>
>   Marc
> --
>  Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
>  mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
>  FAX/Voice +49 697912 39550  -  Tel: +44 1865 275380  or  +33 609 843217
>
>
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust RCD 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

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
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       O