Re: LES analysis

From: Carlos Simmerling <>
Date: Tue 13 Feb 2001 13:39:47 -0500

We are working on improving LES coordinate analysis
for AMBER 7. In the meantime, you have a couple of
choices for LES analysis.You can use my MOIL-View program,
which requires an SGI. It will let you load AMBER
restart and prmtop files and let you watch trajectories
and do some data analysis. You can also save PDB files
or trajectories that include only 1 of the copies.
See my web site link below to get the program.

Another program is downloadable from the moil-view page
as "Carlos's undocumented AMBER analysis program".
This is source code for a simple program that will
let you do things to AMBER coordinates and trajectories.
Most of the features are available in te ptraj module
of AMBER, but this will let you split LES coordinates
or trajectories into sets of files, 1 for each copy.
It is non-graphical and should work on any unix machine.
You can then use those files with other analysis programs.



robert wrote:

> Dear AMBER users,
> I will omit any coments on the last mail received, the one about bras and the like...
> My question is very simple. I would like to know an easy way to analyse restart files
> which have been generated by a multiple copy MD simulation (sander_les).
> Can you tell me where to find a recipe to generate pdbs from those restart files?
> Thank you very much for your help.
> Robert.

Carlos L. Simmerling, Ph.D.
Assistant Professor           Phone: (631) 632-1336
Department of Chemistry       Fax:   (631) 632-7960
SUNY at Stony Brook           Web:
Stony Brook, NY 11794-3400    E-mail:
Received on Tue Feb 13 2001 - 10:39:47 PST
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