Hi,
The 'perrescenter' option just places the target residue and reference
residue at a common reference point based on the geometric center of
the mask atoms. There is no rotation, just translation, so the
orientation of the residue is still what it was after the overall
best-fit RMS that is performed for all selected atoms prior to the
per-residue RMSD calculation.
Hopefully this clears things up - let me know if you have any more questions.
-Dan
On Wed, Dec 12, 2012 at 1:22 PM, Marcus Arieno <marieno.nd.edu> wrote:
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Dec 13 2012 - 08:00:02 PST
