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
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Received on Sat Mar 09 2013 - 18:00:02 PST
