[gmx-users] ligand docking

[Bert de Groot]

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?

Hi,

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).

Bert

____________________________________________________________________________
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
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________