Dear gmx-users,
I am trying to calculate hydrogen bonds with gromacs version 3.3.1 I would
like to have a cutoff of 2.7 A between hydrogen and acceptor and an angle
cutoff of 60 degrees. For that I'm using the following command:
g_hbond -f simulation.trr -s topol.tpr -r 0.27 -a 60 -noda -nonitacc -hbm
-hbn -nomerge
It seems that the cutoff "-a 60" is used on the angle
Donor-Hydrogen-Acceptor instead of Hydrogen-Donor-Acceptor. As a result it
selects hydrogen bonds which are extremely bent and disregards hydrogen
bonds which are almost planar. This is exaclty the contrary of what it
should do. Does anyone have experience in calculating hydrogen bonds with
version 3.3.1?
Thanks a lot,
Gianluca
-----------------------------------------------------
Dr. Gianluca Interlandi [EMAIL PROTECTED]
+1 (206) 685 4432
+1 (206) 714 4303
http://biocroma.unizh.ch/gianluca/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
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