Re: [AMBER] Ligands and cofactors in enzymes

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Tue, 19 Jul 2011 07:58:31 -0300

If you are talking about the minimization of the ligand in antechamber, you *should* expect it to change conformation, basically because its in a different environment than it had in the complex. However, the parameters generated by antechamber are just as valid. You can load those parameters, but use the PDB coordinates for the ligand.

Gustavo.

--
Sent from my iPad.
On 19/07/2011, at 01:54, David Cantu <cantudav.amber.gmail.com> 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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Received on Tue Jul 19 2011 - 04:00:02 PDT