Re: [AMBER] Please solve my problem

From: Adrian Roitberg <>
Date: Tue, 12 Jul 2011 13:18:30 +0200

Dear Elahe.

What proof do you have that the ligand is stable in the active site ?

If it really moves too much, then maybe it should be there in the first
place ?

I do not know what type of restrains you put in there, but if they are
distances, putting two or three different ones should not allow the
ligand to move too much with respect to teh frame of reference of the
active site.

On 7/12/11 1:11 PM, e p wrote:
> Dear Ambers
> 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.
> Thanks for your attention
> Elahe
> _______________________________________________
> AMBER mailing list

                            Dr. Adrian E. Roitberg
                              Full Professor
                Quantum Theory Project, Department of Chemistry
                            University of Florida
on Sabbatical in Barcelona until August 2011.
AMBER mailing list
Received on Tue Jul 12 2011 - 04:30:04 PDT
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