AMBER Archive (2008)

Subject: RE: AMBER: Number of Hydrogen Bonds?

From: Jiapu.Zhang_at_csiro.au
Date: Thu Jan 24 2008 - 19:35:04 CST

Dear Amber friends,

I am also caring about this subject, with one addition: the number of
HBs of the protein with the WATs.

Best regards,
Jiapu

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of d90223013_at_ntu.edu.tw
Sent: Friday, 25 January 2008 12:08
To: amber_at_scripps.edu
Subject: AMBER: Number of Hydrogen Bonds?

Dear all,
Does anyone know how to calculate "the number of hydrogen bonds" vs.
"time" using ptraj ? As far as I know that ptraj is able to track the
interactions between a list of hydrogen bond "donors" and hydrogen
bond "acceptors" that the user specifies. However, it only reveals the
maximum occupancy and lifetimes of a particular H-bond related to the
time series when the option "series hbt" is added to the command line.
Thank you for your help!

Dr. Yi-Ming Cheng

========================
Department of Chemistry,
National Taiwan University
personal site: http://mx.nthu.edu.tw/~ymcheng/
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