AMBER Archive (2006)

Subject: AMBER: Ptraj & pca

From: Claire Zerafa (
Date: Fri Mar 31 2006 - 08:23:05 CST

 Hi everyone,
I am running some pca analysis on the same protein bound to 4 different
ligands and one undocked one. I have worked successfully with doing the pca
analysis on each of the 5 systems, but now I want to plot the rmsd from all
of the 5 trajectories on the same axis so that I can compare these. Each of
my trajectories is made up of 9 tarred files, so I have 45 trajectory files
in all. I stripped the ligand and the box waters from each of these
trajectory files, and read them into ptraj. I did this because I am only
going to use the protein CA atoms for comparison. Then, I referenced these
to a trajectory made representing the average rms fitted trajectory of each
of the individual trajectories i.e. An average of 5 average trajectory files
each of which came from when I performed pca analysis on each of the systems
in isolation. This trajectory file was also stripped of waters and ligand so
that I would have atom agreement. I also generated an average mdcrd file
from the 45 trajectories I read into ptraj. The ptraj terminates fine with
no errors i.e. No atom discrepance warning, but something must be wrong
because I get an error at the pca stage. Does anyone have any ideas? Oh and
I run prtaj with the undocked prmtop file- so there should be no problems
there I guess. Thanks in advance





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