[AMBER] RMSD between two different proteins

From: nicholus bhattacharjee <nicholusbhattacharjee.gmail.com>
Date: Fri, 19 Mar 2010 03:10:04 -0400

Dear community,
                           We know that rms command in ptraj can be used to
calculated the RMSD of different snapshot with respect to some given
structure. Agani some visual sofwares like pymol can be used to calculate
RMSD between two different protein structures a.pdb and b.pdb. Now my query
is that is there a way to find the RMSD of different snapshot of b.pdb
simulation structure from a.pdb i.e at various time step I want to calculate
the deviation of structure of b.pdb from a.pdb. Thanx in advance for

Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Fri Mar 19 2010 - 00:30:02 PDT
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