Hi,
On Tue, Feb 5, 2013 at 11:52 AM, Chinthaka Ratnaweera <cnr88.msstate.edu> wrote:
> rms first out test.dat :N
By default ptraj/cpptraj use best-fit rmsd (the frame is translated
and rotated to minimize the deviation to the reference frame), so you
were best fitting the ligand to itself. What you were calculating was
essentially the internal motion of the ligand.
> I am curious to know what this 'nofit' flag does here.
The 'nofit' keyword tells ptraj/cpptraj not to perform a best fit;
i.e. take the RMSD of the coordinates as they are.
Hope this helps,
-Dan
--
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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/
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Received on Tue Feb 05 2013 - 14:30:03 PST
