From: Irene Newhouse (
Date: Wed May 25 2011 - 14:59:59 CDT

Thank you!
To prepare some inputs, I did a stride 100 of the trajectory just for speed. I'm working with a dimeric protein with 2 ligands in each monomer plus a Mg ion. The ligands & Mg were 'box jumping' independently of each other, so that before treatment there appeared to be ligands in space by themselves, with Mg in another region of space by itself & each protein chain off by itself someplace else. You can see why this scared me:-)
I tried what worked pretty well with the MD of the apo-protein:
package require pbctools
pbc wrap -all -center com -centersel "index 3060" -compound res
I selected index 3060 as being close-ish to the center of mass. It worked! No more Mg, ligands or protein off in space by themselves. Seems the problem is solved!
> Date: Wed, 25 May 2011 09:01:11 +0200
> From:
> To:
> CC:
> Subject: Re: vmd-l: pbctools plugin & protein-bound ligand
> Hi Irene!
> On 05/24/2011 09:36 PM, Irene Newhouse wrote:
> > I have Desmond trajectories I'm analyzing with VMD. The protein is
> > a dimer, and each dimer has 2 ligands bound to it. I know how to use
> > pbctools to unwrap the trajectory so that the dimer units are moved
> > back into the central cell, but the ligands don't move with them.
> > How do I do that?
> Again, it is hard to debug the problem if we do not have access to
> the trajectories - there might be plenty of reasons for your troubles.
> If you want me to help, make the trajectory file available to me, either
> by sending it to me via private email, or putting it somewhere onto the web.
> In this case, could you also provide the commands that you wanted to use
> to achieve what you want? Because you write about "unwrapping the
> trajectory" (which would be "pbc unwrap") and "back into the central
> cell" (which would be "pbc wrap").
> Olaf
> --
> Dr. rer. nat. Olaf Lenz
> Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
> Phone: +49-711-685-63607