From: zoran (
Date: Thu Dec 11 2014 - 06:26:39 CST

Dear Mehdi,
I am novice in namd and vmd but is there really problems to catch the H bonds between P-Wat-Nuc? I think no. What do You really looking for: is that hydrogen bond in-fly along trajectory or You just want to catch these bonds for particular conformational spaces found for max or min energies? If the latter is in quest there are plenty of GUI friendly packages (lets mention free DS visualizer, but also other); its enough to have regular pdb file and You got it without writing any additional script. I note that this stuff does not have any matter with corresponding energies which I suppose should be calculated by the original program.
If the former option is in question it is, what’s up to me, serious omission of either NAMD (if you actually used it) or VMD. I personally run some jobs using MOE and this stuff is so easy to be run along trajectory.

Hope I help You a bit


Dr Zoran D. Matović, professor of chemistry
Head of the Department of Chemistry
Department of Chemistry
Faculty of Science
University of Kragujevac
34000 Kragujevac

Tel/Fax + 381 34 336 223 / 381 34 335 040


Lab for Supercomputing: