Re: [AMBER] cpptraj.hbond: water in the complex

From: Daniel Roe <>
Date: Fri, 1 Jul 2016 11:37:12 -0600


If you want hydrogen bonds between a specific water and solute you can
just specify it in the mask. For example, if my protein is residues
1-220 and I'm interested in water residue 1566, the command would be:

hbond :1-220,1566 out nhbvtime.dat avgout hbavg.dat nointramol

The 'nointramol' keyword will prevent hydrogen bonds within molecules
from being calculated so you will only get the bonds between your
solute and water. This assumes you have imaged your trajectory
beforehand; if not you may want to use the 'image' keyword as well.
This also assumes that particular water never exchanges with the bulk
solvent. If it does, you will have to use the 'closest' command prior
to hbond to keep only the closest solvent molecule to the area of
interest. For example, say I'm only interested in the water that is
interacting with the sidechain oxygen of SER 110:

closest 1 :110.OG first
hbond :1-220,221 out nhbvtime.dat avgout hbavg.dat nointramol

Notice in this case the water becomes residue 221 since all other
waters are stripped away by the 'closest' command.

Hope this helps,


On Thu, Jun 30, 2016 at 7:10 PM, chemjxn <> wrote:
> Dear Sir,
> I apply MD simulation to investigate protein-ligand complex. I use cpptraj script to analysis hydrogen bond surly. The version of cpptraj which I use is ambertools14. The script see the appendix. I would appreciate your help in correct formation of the cpptraj command. I can get the information about hydrogen bond that formed by residue and residue, residue and ligand, residue and solvent water. But what I want is the hydrogen bond between residue and water molecule, the water is included in the complex rather than solvent water. In my system, the water in the complex and the solvent water are both named "WAT". Looking forward to your reply. THANK YOU VERY MUCH!
> Sincerely,
> Liyan
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jul 01 2016 - 11:00:02 PDT
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