AMBER Archive (2002)

Subject: RE: Escaping Atoms

From: case (case_at_scripps.edu)
Date: Thu Sep 05 2002 - 17:04:06 CDT

>===== Original Message From ch cureton <charlie_at_pugh.bip.bham.ac.uk> =====
>I am currently experiencing problems trying to minimise just the waters of
>a solvateOct that surrounds a protein. During minimisation the protein has
>been restrained but consistently I get escaping atoms problems. I am
currently using AMBER 6.0 and am using
>sander_classic for the minimisation.

Why do you want to do 100000 steps of minimization? It should be enough for
most puposes to do 1/100 that many steps, and you could use sander, rather
than sander_classic, which might also help.

...good luck....dac

==================================================================
David A. Case | e-mail: case_at_scripps.edu
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 | http://www.scripps.edu/case
==================================================================