[gmx-users] simulate thiol radical without H

[Daan van Aalten]

After your input, add a line
DELHYD XXX
where you substitute the XXX for the atom name of the sulfur.
This is all also explained in the PRODRG FAQ.
However, this does not egenrate a negative charge, which you'd probably
want so you have to edit the charges yourself.

Daan

On Mon, 16 Feb 2004, Andrea
Guelfi wrote:

> Hi GMXers,
>
> I have a ligand that is not a peptide and has a pKa 8.5, so at
> physiological pH it has a thiol radical without it’s hydrogen.
> I have simulated this ligand with –SH within an enzyme without any
> problem.  I also have used the PrgDrg program in order to find out
> it’s topology.
> I would like to simulate a MD with this ligand without it’s hydrogen
> (only -S). I have tried to have a topology at PrgDrg without this
> particular hydrogen, but it didn’t worked fine.
> Does someone have any idea how to solve this problem?
>
> I appreciate your attention,
>
> Andrea
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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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