Re: [AMBER] Exporting and Boxing Amber Trajectories by Frame

From: Jason Swails <>
Date: Mon, 2 Apr 2012 08:30:16 -0400

On Mon, Apr 2, 2012 at 7:38 AM, Adam Jion <> wrote:

> Hi!
> I'm using Amber for a non-routine molecular dynamics simulation on the
> crystallization of glycine zwitterions in a triclinic box.
> I would like to export each frame of the trajectory as .pdb file with only
> the glyzine zwitterions extracted. That is, I will be exporting about 10000
> individual .pdb files with each file containing only glycine zwitterions.
> Furthermore, each glycine zwitterion should be translated back into the
> box.
> Is this possible with Amber's ptraj command?

Yes. The "image" command will map all of the molecules back into the
periodic box around the point you're imaging.

e.g. "image origin familiar" (the familiar is for the triclinic box).

Then you can strip away all atoms you don't want, and write a series of PDB
files using 'trajout'.

The manual should describe all of this fairly thoroughly.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Mon Apr 02 2012 - 06:00:05 PDT
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