AMBER: Dynamics and Restraint problem

From: Andrew Box <>
Date: Mon, 17 Jul 2006 23:49:51 +0000

Amber Users

I have an error with using noe restraints with Amber 8.0. When i construct
the constraint file, all looks fine, and when i run the file in a dynamics
run, the runs proceeds to completion. But when i check the output file, the
noe violations are have the incorrect atom names. This problem only occurs
in Amber 8.0 (which is the version i am currently running, and is also
available on our local super computer). When i perform the runs in Amber
7.0, i had no problems, and i also tried to use the file i generated in
Amber 7.0, and i get the same result.

Have any changes been made to how constraint file are generated or read
since Amber 7?

I have included with this the:
map file - map.AMBER3
the pdb file - b2.pdb
7 column constraint file (before i ran it through makeDIST_RST) - DIST4
output file: md5.out
restraint file - RST2 (Amber *) and RST2_old (Amber 7)

Thanks in advance.

Andrew Box
La Trobe University
Melbourne, Australia.

Be the one of the first to try the NEW Windows Live Mail.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to

Received on Wed Jul 19 2006 - 06:07:09 PDT
Custom Search