Re: [AMBER] MMPBSA Energy between system and its image

From: Jason Swails <>
Date: Fri, 4 Jul 2014 15:29:16 -0700

On Fri, Jul 4, 2014 at 2:15 PM, Ahmed Ayoub <> wrote:

> Hi Jason,
> Thanks for your help. I just want to make sure of something. Do you have an
> easy way of creating the topology files for the two subunit system? I'm
> thinking of replicating the system using, maybe, PropPDBmodule and taking
> it to tleap. Is that fine?
> Also the processing of the trajectory to contain only the two images I'm
> interested in; do you know of an easy way yo do it? Is there a way in ptraj
> I can do it?

cpptraj can strip atoms from the system very simply, but it has no
functionality to add new atoms that I'm aware of. As I said in my last
email, I know of no tools that can automate what you are trying to do.
 PropPDB can propagate a PDB file, but not an entire trajectory (or any
other type of file). You may be able to coerce it into duplicating the
system the way you want (but you may want to determine which periodic image
is the 'closest' in terms of the one propagated in the x, y, or z
direction), but you will need to work exclusively with PDB files in that

You will still need to create a topology file to match the propagated
system if you want to compute any energies, though. You will likely have
to experiment with different tools and different protocols to design an
effective workflow, and you will probably have to write some scripts and/or
programs to supplement the functionality that is not available elsewhere.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Jul 04 2014 - 16:00:02 PDT
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