VMD-L Mailing List

From: YangMingjun (mjyang_at_dicp.ac.cn)
Date: Mon May 18 2009 - 08:14:38 CDT

Dear all,

   I am going to setup a model of protein A1 for MD simulation. But pdb of A1 is determined in apo form. Now I want to place the ligand, a GTP molecule, into A1. There is another homologous A2 structure in complex with GTP. The binding pockets of A1 and A2 are highly conserved and have much similarity in conformation. When aligning A1 to A2 with the conserved region, I get a model of A1 with the ligand docked into. My question is how should I do to optimize the built model to get a reliable initial model for MD simulation? Though the binding pockets are highly conserved, the apo- form and the GTP-binding form are not all the same. So some appropriate optimization is necessary and required. But I don't know which is the best way and which software I should use for this purpose?

Request your suggestions.

Many thanks.

Mingjun