From: Markus K. Dahlgren (
Date: Mon Oct 10 2011 - 15:09:35 CDT

Hi Elia,

Yes I tried using pbc unwrap, but that does not solve the problem. I ran pbc
unwrap with the following command:

pbc unwrap -first now -all

I then ran the RMSD trajectory tool. Out of 40ns simulation, the ligand is not
placed inside the protein for 10ns. This is an alignment problem that I have
not been able to fix with either pbc unwrap or the trajectory tool. If I have
the selection: resname UNK in trajectory tool, then the ligand-protein complex
is centered and aligned, but the protein is rotationg around the ligand as the
trajectory proceeds. Ideally I would have the protein centered and
aligned with
the ligand so that the protein structure is constantly centered.

Any tips on how to do this would be greatly appreciated.


Quoting "Zumot, Elia Nabil" <>:

> 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
> To:
> Subject: vmd-l: centering problem in trajectory tool
> Hi,
> 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!
> Markus