Hi,
This seems like an imaging issue. Did you try to re-image your
trajectory at all? I recommend using the 'autoimage' command from
AmberTools 12 cpptraj to image your trajectory prior to running your
RMSD calculation.
-Dan
On Sat, Mar 9, 2013 at 6:55 PM, Kira Armacost
<kza0004.tigermail.auburn.edu> wrote:
> I have performed an RMSD calculation on a few 300ns trajectories and noticed that the RMSD plots didn't look right. I had spikes from 5 Angstroms to 11 Angstroms, one frame apart, so I pulled the pdb's from those frames and noticed that the ligand was not in the active site of the enzyme for that frame. I checked a few pdb's and only a few of them do that. On these trajectories I have also performed other calculations in ptraj (distance - including ones with the ligand, clustering and hydrogen bond) and only have this error when I perform RMSD. Here's my input script:
>
> trajin xx.crd.gz
> rms first out rmsd.out time 0.01 :1-362
>
> I have noticed this problem before when I stripped the water from the enzyme for analysis, but in this case, the water is still there.
>
> Thanks!
>
> Kira A. Armacost
> Ph.D Candidate
> Department of Chemistry and Biochemistry
> Auburn University
> Dr. Orlando Acevedo Research Group
> Concepts of Science GTA
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Sat Mar 09 2013 - 20:00:03 PST
