From: David A. Case <>
Date: Wed, 28 Mar 2012 10:53:38 -0400

On Tue, Mar 27, 2012, Olena Dobrovolska wrote:
> in the final results part there is this COM instead of the a certain
> atom name as it should be.

Can you be more specific? I don't see any "COM" in the final results section
of your output. COM stands for center of mass, and you have lots of groups of
atoms (mostly methyls) where the constraint is to the center of mass of
several atoms.

> I also have a huge (663) distance penalty
> value, although the CYANA output files, used in AMBER as inputs, have
> target function around 4, and RMSD 0.5.

You total distance penalty is made up of many values that are 20 or 30 or
so, with only the sum coming up to 663. You probably need to examine the
biggest restraint violations(which involve distances of about 1 Ang) to
see if there might be typos in the RST file, or similar problems.

Good luck....dac

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Received on Wed Mar 28 2012 - 08:00:05 PDT
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