AMBER Archive (2009)

Subject: Re: [AMBER] RST file

From: David A. Case (
Date: Fri Apr 10 2009 - 07:21:19 CDT

On Thu, Apr 09, 2009, waleed zalloum wrote:
> I am running a restrained simulated annealing. in my RST file
> I noticed that  a 2 angstroms were added to the upper and
> lower limits of a distance between a pseudoatom and a any other
> atom.  Distances between non-pesudoatoms are OK. Is that a normal
> thing, or there is problem in my file?

There are lots of ways to prepare restraints, and one cannot tell from
your question which method you used. Generally, using pseudoatoms
increases the bounds (to account for the ambiguity involved). You may
need to study the source code of makeDIST_RST.c (if you used that
program) to see exactly what is going on.


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