AMBER Archive (2004)

Subject: Re: AMBER: Re: ANAL problem

From: David A. Case (
Date: Thu Feb 05 2004 - 11:36:05 CST

On Wed, Feb 04, 2004, A.B.S.M Osman gani wrote:
> 1)I have used same prmtop file for running dynamics.

It looks like your prmtop file uses a truncated octahedron (which I am not
sure that anal will recognize). Also, you seem to have used ptraj to remove
the box information from the coordinates, but you did not change the prmtop
file accordingly.

Here is my suggestion (maybe others have better ones): use ptraj to strip
out the waters (if you are not interested in them), and to create a new
prmtop file that is missing the waters (see the "stripwater" command in
rdparm). Then try anal again with this smaller, nonperiodic system.

..good luck...dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to