AMBER Archive (2003)

Subject: Re: AMBER: Protein Rotation

From: volodya (volodya_at_imb-jena.de)
Date: Sun Oct 12 2003 - 08:40:07 CDT

Dear Frederico Miranda,

Can you write your input file. I am looking for my work. I asked AMBERs
users before about this, but, unfortunately, I have not received answer.

Sincerely yours,

volodya

Frederico.Miranda_at_ibmb.uib.no wrote:

>Hye, I made a MD simulation for a protein, and used carnal to determine RMS
>for each residue, but my protein is rotating during the MD, so I have a great
>discrepancy in the values. Is there a way that I could remove the effect of
>the rotation when doing the calculation?
>
>Thank you.
>
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-- 
Volodymyr Nechiporuk-Zloy
Institute of Molecular Biotechnology <http://www.imb-jena.de>
Dept. Single Cell and Single Molecule Techniques 
<http://www.imb-jena.de/www_kog/>
Beutenbergstrasse 11
D - 07745 Jena
Germany
Phone: *49 3641 656169
Fax:      *49 3641 656166

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