Re: [AMBER] hydrogen bond evaluation

From: Daniel Roe <>
Date: Mon, 14 Jul 2014 10:05:51 -0600


On Mon, Jul 14, 2014 at 9:49 AM, Jason Swails <>

> That said, I highly suggest that you upgrade to AmberTools 14 and switch to
> using cpptraj instead. The hbond command has been drastically simplified.

I second this. Your entire PTRAJ script could be one command in CPPTRAJ,

hbond H1 donormask :1-64.O= acceptormask :1-64.O= nointramol \
  solventdonor :WAT solventacceptor :WAT.O \
  out numhb.dat avgout avghb.dat solvout avgsolvent.dat bridgeout bridge.dat

I definitely recommend reading the manual to get an idea for what keywords
are available for the hbond command in CPPTRAJ and what they do. Good luck,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Mon Jul 14 2014 - 09:30:02 PDT
Custom Search