[AMBER] ptraj minimum rmsd in presence of homotopic atoms

From: Alexander Metz <alexander_metz2000.yahoo.de>
Date: Tue, 29 Mar 2011 10:21:21 +0100 (BST)

Dear AMBER community,

I am currently using ptraj to calculate RMSD values of docking poses. I actually
would want to calculate the minimum RMSD in the presence of homotopic atoms in
my molecule. In other words, for RMSD caluclation the equivalent atoms of a
phenyle group should be treated in a way that a 180° rotation of the ring does
not change the RMSD. Actually in ptraj each atoms seems to be treated as a
distinct entity with distinct name, id, etc. ... also with respect to RMSD

Is there any way to get this kind of minimum RMSD easily? I could rename all
atoms to create a set of structures where all homotopic atoms are interachanged
and then caluclate the RMSD.

Best regards,


Alexander Metz (PhD Student)
Heinrich Heine Universität Düsseldorf
Institut für Pharmazeutische und Medizinische Chemie
Computational Pharmaceutical Chemistry
Universitaetsstrasse 1
40225 Düsseldorf, Germany
Tel: +49 211 81 13854

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Received on Tue Mar 29 2011 - 02:30:03 PDT
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