Re: [AMBER] Dynamic selection of donor and acceptor mask for hbond analysis

From: Daniel Roe <>
Date: Fri, 15 Aug 2014 13:52:50 -0600


With the exception of the 'mask' action distance-based masks do not
update on a per-frame basis in cpptraj as this could lead to the
topology constantly varying through the course of a trajectory, making
bookkeeping a nightmare. You can retain a fixed number of waters with
the 'closest' command, but I don't think this is what you want.
Cpptraj is not currently set up to really analyze solvent-solvent
hydrogen bonds. You can make cpptraj do it by explicitly specifying
water with the 'donormask'/'acceptormask' keywords and using the
'nointramol' keyword, e.g.:

hbond hb donormask :WAT acceptormask :WAT.O nointramol out solvhb.dat
avgout solvavg.dat

However, this will report hydrogen bonding explicitly between every
single water, which will be a ton of data unless you're using a
relatively small selection of waters. Of course you could then
post-process that output, but I'm still not sure that's what you need.


On Fri, Aug 15, 2014 at 4:11 AM, DEBOSTUTI GHOSHDASTIDAR
<> wrote:
> Dear Amber users,
> I was wondering if we could perform a hydrogen bond analyses on a dynamic
> selection of donor and acceptor molecules (e.g, hydrogen bonding between
> water in the hydration shell of a protein). I tried using the distance
> based mask selection available in cpptraj of AmberTools14 but it seems all
> the water in the system get selected and not just the hydration shell water.
> Thanks
> --
> Debostuti
> _______________________________________________
> 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 Aug 15 2014 - 13:00:02 PDT
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