[gmx-users] ATP TOPOLOGIES

[Daan van Aalten]

Dear Raj

This is interesting. Are you sure you are using not only the topology file
that comes from the PRODRG server, but also the GROMACS coordinate file
produced by the server, *NOT* the one you put into the server in the first
place? Do you put coordinates into the server (if so, could you send
them), or do you provide a drawing (much preferred)?

cheers

Daan

On Tue, 16 Dec 2003, Raj Badhan wrote:

> Hi
> Does anyone have a working topology of ATP which has NOT been
> created using PRODRG?
> My ATP from PRODRG seems to not like my simulations and I
> would like to try another version of it. Sadly, I am a novice at
> gromacs and am hvaing problems creating my own topologies.
> Thanks for the understanding and advice from David and others.
> Cheers
> Raj Badhan
> Postgraduate researcher
> School of Pharmacy and Pharmacetical Science
> The University of Manchester
> Manchester, UK.
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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

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