AMBER Archive (2009)

Subject: Re: [AMBER] HB for each snapshot

From: Nicolas Sapay (
Date: Thu Nov 05 2009 - 02:30:51 CST

Marcin Krol a écrit :
> Hello,
> A couple of weeks ago I asked whether ptraj can tell me the presence
> or absence of HB for each snapshot of a trajectory between a given
> pair of residues. Using hbond facility I can get occupancy and a
> graphical representation showing schematic of time-series, but what I
> really need is the HB information for each snapshot. I'm sure ptraj
> generates this info (to get the occupancy, etc), but I don't know how
> to get it. Please let me know i if I can get _per snaphot_ analysis of
> HBs in ptraj, it'll save me lots of work.
> Or maybe you can suggest another program to perform such analysis. Any
> help appreciated

It is relatively straightforward to calculate the number of H bonds with


> Thanks in advance
> best
> Marcin

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