AMBER Archive (2009)

Subject: RE: [AMBER] Hbond analysis output giving no hbonds

From: Thomas Cheatham (
Date: Tue Nov 24 2009 - 10:58:27 CST

Try adding the "out" keyword...

hbond series hbt out hbond.dat \
   time 1.0 angle -1.0 distance 3.1

> I am trying to get Hbond analysis using ptraj of an MD run. Since the
> protein is large, the memory needed was huge. So, I am trying to call
> subsets of atoms to reduce memory requirement. It looks like the run is
> going to completion successfully, but the output does not show any Hbonds. I
> am attaching the input and output files. Help is greatly appreciated. Thank
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