Re: [AMBER] Please solve my problem

From: Carlos Simmerling <>
Date: Tue, 12 Jul 2011 07:20:22 -0400

How can you be sure that the initial docked position is fully correct? Do
you know that the lugand is stably bound prior to the reaction? Are you sure
the parameters for the ligand are good? There are many questions for which
you are the only one that can best answer them.
 On Jul 12, 2011 7:12 AM, "e p" <> wrote:
> Dear Ambers
> I want to inspect the effect of connection of a ligand to my protein
> 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
> 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
> want to use restraints to limit active site vibrations.
> Any offer would be apprecited.
> Thanks for your attention
> Elahe
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Received on Tue Jul 12 2011 - 04:30:04 PDT
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