[gmx-users] editing parameters

[Daan van Aalten]

Hi Regina

Have you tried the PRODRG server for you rligand?

http://davapc1.bioch.dundee.ac.uk/prodrg

charge calculation with QM programmes is an excellent idea - as long as
you stick to the charge group concept (David - could you comment on this
please?)

cheers

Daan

On Wed, 7 May 2003, Regina R. Monaco, Ph.D. wrote:

> I am setting up a run to do a MD calculation, which includes a ligand
> (ethidium cation) that pdb2gmx doesn't recognize.  Ethidium doesn't
> contain any oddly-parameterized atom types.  I have used gaussian to
> calculate the ethidium charges, but am not sure how to import those
> charges into the parameter files. Various error messages received while
> trying to run pdb2gmx have been (depending on force field tried):
>
> Fatal error: Atom C1 in residue ETH not found in rtp database   **OR**
> Fatal Error: Residue "ET" not found in residue topology database
>
> as examples.
>
> What is the procedure for editing the rtp ?
>
> Thanks,
> Regina Monaco
>
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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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