[modeller_usage] modelling with ligands (FAD FMN and NADP)
Subject: [modeller_usage] modelling with ligands (FAD FMN and NADP)
From: Yerko Escalona <>
Date: Mon, 16 Nov 2009 23:58:31 -0300
Hi I have a problem when i model the structure of proteins with ligands (hetatm = NADP, FAD and FMN), because some residues have improper bond, like the Asparagine make bond between the N and C(gamma), or Phenyalanine with wrong position of aromatic carbon.
I try resolve this with the optimization of models with VTFM and MD&SA but the error in the bonds of residues is the same. Also try without ligands and that's work. I think the problem is of the ligands that make incorrect restriction to the protein and make that errors.
I hope that you can help me. Bye
(My native language is the Spanish, so sorry for the mistakes)