[AMBER] Ligands and cofactors in enzymes

From: David Cantu <cantudav.amber.gmail.com>
Date: Mon, 18 Jul 2011 23:54:50 -0500

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,

AMBER mailing list
Received on Mon Jul 18 2011 - 22:00:02 PDT
Custom Search