Re: [AMBER] ligand & protein with dist restraint

From: Dmitry Nilov <>
Date: Tue, 12 Jul 2011 15:30:35 +0400

I would restrain the distance between ligand atoms involved in
catalysis and active site residues at the equilibration stage. What is
the reason to apply restraint on atoms that are not involved in

> I want to inspect the effect of connection of a ligand to my protein before
> formation of a covalent bond to the active site. I have designed a  new
> ligand and put it to the active site by auto dock. the ligand moved during
> MD run so I had to put dist restraints(rk2=50,) on ligand atoms that are not
> involved in catalysis and on 5 residues of the protein out of the active
> site. it didnt solve the problem. the ligand still moves and rotates.As I
> want to study the vibrations before formation of nucleophilic attack, I dont
> want to use  restraints to limit active site vibrations.
> Any offer would be apprecited.
> Elahe
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Dmitry Nilov
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
AMBER mailing list
Received on Tue Jul 12 2011 - 05:00:03 PDT
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