AMBER Archive (2006)

Subject: AMBER: hbond analysis

From: Vlad Cojocaru (
Date: Tue Oct 03 2006 - 10:45:23 CDT

Dear Amber users,

I am trying to use the ptraj hbond facility to analyze lifetimes of
hydrogen bonds in a protein and between a protein and a ligand. More
precisely, I am trying to define a set of donors and have ptraj printing
out all Hbonds formed by these donors in at least 1 frame of the
trajectory (with the donor-acceptor distance, angle, occupancy etc -
see script below). However the output of this script is null. Maybe
somebody can give me a hint what am I doing wrong here.

I used to do this type of analysis with CARNAL and it always worked
pretty nice but since now I am using ptraj for almost all analysis, I
thought of using ptraj for this one as well. However, all the examples
that I found an the amber archive were about solvent interactions in
which the definition of donor and acceptors were exact.

Best wishes

trajin file.mdcrd
donor mask
acceptor mask :1-467_at_O* @H*
hbond distance 3.2 angle 60.0 series hbonds.dat

Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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