[AMBER] RMSD Calculation

From: abc def <biotechabc.gmail.com>
Date: Fri, 18 Mar 2011 22:17:41 +0530


I want to know that how RMSD calculation is done in amber? Does it use
Kabsch algorithm? Does it take into account the symmetry correction while
computing RMSD as in the AutoDock? Actually I wanted to understand how can
one compute RMSD taking into account the symmetry of the ligand. That is if
the ligand is rotated upside down by 180 it is symmetric to its previous
configuration but however the atom positons have changed. I calculated RMSD
using VMD but its coming out to be 1.6 where it should have been 0.0 as the
molecule exactly overlaps with the original one? Can anyone suggest me some
stand alone tool which does RMSD calculation between the reference complex
and the other complex but may require symmetry calculation while computing
RMSD. I would also like to know that how such a thing is done - algorithm.

Thanks in anticipation,
Pooja , india
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Received on Fri Mar 18 2011 - 10:00:04 PDT
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