[AMBER] ligand & protein with dist restraint

From: e p <epepgene1.gmail.com>
Date: Mon, 11 Jul 2011 07:08:10 -0700

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.

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Received on Mon Jul 11 2011 - 07:30:03 PDT
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