Re: [AMBER] Ligands and cofactors in enzymes

From: Dmitry Nilov <>
Date: Tue, 19 Jul 2011 10:06:13 +0400

Hello, you can apply position restraints to protein and ligand atoms
during the minimization.
Note, that parameters, automatically derived by antechamber can be
incorrect. That can be the source of the problem.

On Tue, Jul 19, 2011 at 8:54 AM, David Cantu <> wrote:
> Dear Amber Users and Developers:
> I have a general question about placing a ligand (or cofactor) in the
> correct position and conformation inside an enzyme's active site.
> Suppose you have a ligand (LIG) crystallized in an enzyme. You take LIG's
> coordinates, add hydrgens, run it throough antechamber, make the mol2 and
> frcmod files. But during minimizations its conformation was changed.
> What I want to do is keep the crystallized conformation of LIG (not the
> minimized in the mol2), plus hydrogens. What needs to be done in Leap to
> load LIG in its crystallized conformation, but use the parameters derived
> from antechamber for GAFF?
> Thank you,
> David
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Dmitry Nilov
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
AMBER mailing list
Received on Mon Jul 18 2011 - 23:30:03 PDT
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