AMBER Archive (2006)

Subject: Re: AMBER: PTRAJ OUTPUT

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Jul 05 2006 - 18:43:57 CDT

> I have performed hbond analysis on 5 ligand protein complexes which are
> identical except for the ligands, and have gotten no error messages. These
> complexes were subjected to 1800ps dynamics in sander and all contain an
> average of 25000 atoms. ptraj has outputted results, and no error messages,
> however, when I look at the output files, for one complex, a significantly
> smaller number of data sets was read in- 3198 vs 3600 for the others. Since
> the trajectory time is identical, I can see no reason why this should be
> so... I was wondering whether anyone could help me please...
 
Is there any chance that you used a wrong prmtop/trajectory
combination? Or that one of the md runs crashed?

Bill
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