AMBER Archive (2002)

Subject: Sander-Gibbs

From: Kidley N J (njkidl_at_essex.ac.uk)
Date: Mon Apr 08 2002 - 10:34:49 CDT

Dear Sir/Madam,

I am trying to run some simulations using the Sander and Gibbs programs. I
have been lead to belive that you can switch between the two, (ie minimise
then warm up the system, then do the free energy pertubation, etc). But I
seem to be having input file format problems, and just get error messages
stating that the format is either not supported, or one that states the
PARM TOPOLOGY is set to run with GIBBS only.

I am using AMBER5 and AMBER6, so I would like to know if it is possible to
use these programs like this, and if not does anyone know how I could
essentially perturbe the system with the NOESY restraint opition
activated.

Yours faithfully

Nathan Kidley

Biological Sciences Dept
University of Essex

email: njkidl_at_essex.ac.uk