When running g_hbond -h, I see the following, among other things:
-[no]da bool yes Use distance Donor-Acceptor (if TRUE) or
Hydrogen-Acceptor (FALSE)
Hope that helps.
Erik
Nilesh Dhumal skrev 2011-04-11 23.05:
Is it possible to find number of hydrogen bonds using g_hbond by
considering the distance between Acceptor-hydrogen instead of the distance
between Acceptor-Donor atoms.
Nilesh
On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote:
Try the -contact option.
Erik
Nilesh Dhumal skrev 2011-04-11 17.12:
Is there any way to specify clorin and florin atoms as a receptor.
Nilesh
On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I am trying to calculate number of hydrogen bond (O-H---CL)in my
system.
I use the following command
g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num
Output file hbnum.xvg shows zero number of hydorgen bond.
Can you tell me why its showing zero no.
A strong peak is found in rdf between H and CL at 2.0 A.
Chlorine is not considered a receptor in g_hbond.
-Justin
I am using Gromacs 4.0.7 version.
Nilesh
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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