AMBER Archive (2006)

Subject: AMBER: Dynamics and Restraint problem

From: Andrew Box (box_twin3_at_hotmail.com)
Date: Mon Jul 17 2006 - 18:49:51 CDT

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.

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  • application/octet-stream attachment: DIST4

  • application/octet-stream attachment: md5.out

  • application/octet-stream attachment: RST2_old

  • application/octet-stream attachment: RST2

  • application/vnd.palm attachment: b2.pdb

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