[gmx-users] EM of a single molecule

[Daan van Aalten]

Dear Tanos

PRODRG on the server automatically energy minimises the ligand with
GROMACS (unless you use the button to switch that off).
If you download the tar.gz file it generates
for your ligand you should also find in there the GROMACS input files for
this. These may give you some help in deciding what to do.

cheers
Daan

On Tue, 16 Dec 2003, Tanos wrote:

>     Hi folks,
>     I wish to perform a EM of my cofactor alone (separated from the
> protein's active site). I have already parametrized the cofactor in the
> Dundee site and have got my .gro and .itp files but I am not been able
> to run the energy minimization in GROMACS with this files. Can someone
> help me. All I want is to perform a EM of a single molecule (different
> of a protein) in a water box.
>     Thanks a lot in advance.
>     Tanos C. C. Franca
>     IME - Rio de Janeiro
>     Brazil
>
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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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