AMBER Archive (2008)

Subject: Re: AMBER: problem with traj and strip waters

From: David A. Case (
Date: Thu Sep 18 2008 - 08:34:18 CDT

On Thu, Sep 18, 2008, Steve Seibold wrote:
> 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;

Did you try the "nobox" option anyway? Note that the box information is
not just "at the end" of the trajectory. If the (no-water) prmtop file
does not have box info, then you must use the nobox parameter in your
trajout line.


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