AMBER Archive (2009)

Subject: [AMBER] HB for each snapshot

From: Marcin Krol (
Date: Wed Nov 04 2009 - 13:14:41 CST


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

Thanks in advance

Dr Marcin Krol
Zaklad Bioinformatyki i Telemedycyny
Collegium Medicum Uniwersytet Jagiellonski

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