From: Bill Ross <>
Date: Wed, 5 Jul 2006 16:43:57 -0700 (PDT)

> 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?

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jul 09 2006 - 06:07:10 PDT
Custom Search