AMBER Archive (2008)

Subject: Re: AMBER: GBSA SA calculation

From: David A. Case (
Date: Wed May 07 2008 - 16:17:07 CDT

On Wed, May 07, 2008, Titus, Jamie (bairdje) wrote:
> I am currently trying to extract SA terms from a trajectory which I have
> stripped of H2O and ions,

Did you use the "nobox" parameter in the trajout command when you stripped the
waters and ions? Forgetting to do this is the most common cause of problems:
your trajectory may have box information that the trajene code is not

Of course, if you *did* use nobox, then the problem is probably somewhere
else. A good test is to use ptraj to read in and analyze some feature, using
your stripped trajectory and the new prmtop file, to make sure they are
compatible with each other.

(Carlos: are we getting closer to having a patch for trajene that incorporates
Dan's changes?)

...good luck...dac

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