AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Nov 23 2006 - 11:25:31 CST

use the trajout command, it will write pdb files with a numbered extension.
you need to specify the "pdb" option to trajout- check the ptraj section
of the manual.

Jordi Rodrigo De Losada wrote:

> Dear Amber users,
>
> 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?
> Does anybody could help me and give the command or the little script
> for this?
> Thank you very much in advance.
>
> Jordi
>
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