[gmx-users] ATP TOPOLOGIES

[Daan van Aalten]

Dear Raj

If the topology works fine with EM of the compound on its own, then the
fault lies not with the ATP topology, but the way you incorporate it in
the overall topology of your enzyme-ligand system. How to do is is very
clearly defined in John's tutorial. Perhaps you should try as a test a
different system first. Also you should *NOT* call your molecule "ATP",
otherwise GMX will get confused as it does have an ATP topology predefined
in its own forcefield files.

Daan

On Tue, 16 Dec 2003, Raj Badhan wrote:

> Dear Daan,
> Thank you for replying to my e-mail.
> I extract ATP from a PDB file, use the ATP coord to input into
> prodrg and then use the GRO and ITP files returned from prodrg to
> input into my protein.
> find attached the input PDB and output GRO.
> When I add the output gro into my protein gro, and solvate the box,
> the ligand is broken down into its individual atoms and spread
> outwards from the protein.
> This also occurs when running an EM.
> I can get this to work on ATP alone, but not when in the active site
> of my protein.
> Any advice would be appreciated.
> Many thanks
> 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

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