From: Olaf Lenz (
Date: Wed May 25 2011 - 02:01:11 CDT

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").


Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
Phone: +49-711-685-63607