From: Zumot, Elia Nabil (
Date: Mon Oct 10 2011 - 11:19:48 CDT

Hi Markus,

Have you checked the pbc wrap options in VMD?

Elia Zomot, PhD
Computational and Systems Biology Department
School of Medicine, University of Pittsburgh
3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
Voice: 412 648 7785 - Fax: 412 648 3163
From: [] On Behalf Of Markus K. Dahlgren []
Sent: Monday, October 10, 2011 9:59 AM
Subject: vmd-l: centering problem in trajectory tool


I have modeled a protein-ligand complex with explicit waters and during the
simulation there is center of mass movement. The complex was simulated using

When I align the complex with the protein selection in the trajectory tool in
vmd, the ligand is not centered/aligned with the protien for about 40% of the
trajectory. If I align the complex with the resname UNK selection (ligand
residue name), the trajectory becomes very painful to look at as the protein
keeps rapidly moving around the centered ligand.

The ligand is fairly large and has a 10-unit peg linker, which likely causes the
alignment problem when the linker part of the ligand crosses into the next
periodic boundary box.

What can I do to center and align the ligand-protein complex so that I can view
it in VMD?

Any help would be greatly appreciated!