AMBER Archive (2006)

Subject: Re: AMBER: Unstable RMS trajectory

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Tue Oct 17 2006 - 11:46:48 CDT

Did you rms fit the trajectory before attemping to compute the rms ?
otherwise you are looking at an rmsd going up simply because of difusion.

Also: are you sure you are computing rmsd for JUST the protein and NOT
the water atoms ? 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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