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
calculations.
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
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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
