AMBER Archive (2004)

Subject: Re: AMBER: snapshots of MD trajectory

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Fri Aug 27 2004 - 10:36:38 CDT

try ptraj, it is documented in the AMBER manual.
moil-view also does this but only for SGI machines.
both are on the AMBER cd.

===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Xin Hu wrote:

> Hello,
> I have a question about the analysis of MD trajectory from Amber 8.
> How can I extract all the snapshots (such as save as PDB file) from
> the MD trajectory, and generally, is there a way to cluster these
> ensembles of MD snapshot?
>
> Thank you very much for your help.
>
>
> Xin
>
>
> ---
>
>
>
>

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