[gmx-users] ligand docking

Bert de Groot bgroot at gwdg.de
Wed Mar 6 14:49:15 CET 2002

jozef hritz wrote:
> I would like to dock ligand to protein. I know 2 distances between
> ligand_atom1 -- protein_atom1
> ligand_atom2 -- protein_atom2
> in final structure.
> So my plan was let to ligand difuse from outside to binding place using
> this two distance_restraints. I asked in mailing_lists if it is possible
> to aplly distance_restraints between two atoms of two different groups,
> but I haven't got any answer so probably it's not possible.
> Then I started study mailing list about pull code.
> When I understood well, there were problems with pull code (Justin).
> The question is how it looks now, does it work better and is it possible
> to use it on my problem, to aply 2 springs between two atoms of ligand and
> two atoms of protein?
> Or should I use some other tool?


I don't know too much about distance restraints or the pull code in gmx, but
one quick&dirty approach to your problem would be to fix the center of mass
of the protein, and use a mild position restraint for the ligand with
as target position the binding pocket (defined from the two distances you have).


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de

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