AMBER Archive (2008)

Subject: AMBER: problem with traj and strip waters

From: Steve Seibold (
Date: Thu Sep 18 2008 - 08:08:21 CDT

Hello Amber

I am having a similar problem which I have had in the past, but this
time I cannot seem to over come it. I have combined trajectories and
have performed an rms analysis without any problem. However, once I
strip the waters off and try to perform an rms analysis, I get absurd
values (70 angstroms and greater). I thought maybe I should use the
"nobox" but there is no box information at the end of the trajectory
files after I strip the water out; so, this is not causing the problem.
In addition, there is no error or corrupt files mentioned in the output.
I am also using a topology file that has had all waters removed (using
xleap). Does anyone have any ideas about what is happening?

Of course, I could just do rms evaluation with water present, but this
takes so long. Thus, I would like to strip the water from the


Thanks, Steve

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