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.
...dac
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Fri Sep 19 2008 - 03:10:18 PDT
