Hello AMBER list,
The Ambertools 12 manual describes the 'perrescenter' option while
performing a per-residue RMSD calculation in cpptraj as the following:
"If perrescenter is specified residues will be centered to a common point
of reference before no-fit RMSD is calculated (this will emphasize changes
in the local structure of the residue)."
Does anyone happen to know exactly how this 'perrescenter' option first
centers each residue to a common point? Is each residue centered by
best-fitting to itself, or perhaps centered by best-fitting to the residue
and those geminal to it? Any clarification is helpful!
-Marcus Arieno
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Received on Wed Dec 12 2012 - 12:30:03 PST
