AMBER Archive (2006)

Subject: Re: AMBER: Snapshots (pdbs) from a trajectory.

From: David A. Case (
Date: Thu Nov 23 2006 - 21:58:34 CST

On Thu, Nov 23, 2006, Jordi Rodrigo De Losada wrote:
> I'm planning to obtain some snapshots(in PDB format) from a dynamics. In
> the previous versions of Amber I used the CARNAL module in order to get
> these pdbs. I've tried to find in the manual how to get this snapshots
> using ptraj. I saw that I can get an average of my dynamics and also
> analyze the results, however, I didn't find how to obtain some snapshots.
> For instance, if I run a dynamics of 250 ps and I want to recover a pdb
> file every 10 ps (so 25 pdbs at the end) what command or module should I
> use?

Something like this:

   trajin <filename> 10 250 10
   trajout <pdb-filename> pdb

The first line takes every 10th snapshot (starting from number 10, ending at
number 250). If your trajectory has a snapshot every picosecond, this would
do what you want. If your trajectory has a different time interval, modify

The second line saves the snapshots in PDB format.


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