Re: [AMBER] Bridging Sodium ions using hbond

From: Daniel Roe <>
Date: Mon, 1 Sep 2014 09:11:54 -0600


On Mon, Sep 1, 2014 at 4:36 AM, DEBOSTUTI GHOSHDASTIDAR
<> wrote:
> hbond out test1.dat solventdonor :Na+ solventacceptor :1-24.O1P,O2P
> nointramol solvout test.dat (where 1-24 are the residue numbers of the DNA
> dodecamer)

This isn't the correct way to use Hbond to track ions. You want both
solvent masks set to ions, then provide another mask (or use the
donormask/acceptormask keywords) for the solute, e.g.

hbond out test1.dat solventdonor :Na+ solventacceptor :Na+ \
    :1-24.O1P,O2P nointramol solvout test.dat

Also, be careful that you are using the correct atom names. The
phosphate oxygens may be named OP1/OP2. You can check this easily by
running cpptraj with the '--mask' command-line flag, e.g.:

cpptraj <topology file> --mask '.O1P'

Hope this helps,


> In the output, however, I see that test.dat contains not only hbond
> information between the O1P/O2P with Na+, but also those formed between
> other atoms of the DNA and Na+.
> Hence, I assume that the information on solvent bridges given in the
> test1.dat file include Na+ ions that bridge any two atoms of the DNA and
> not just the phosphates.
> Any suggestions on how I can get the required information, i.e, only Na+
> ions that bridge the phosphates?
> Thanks
> --
> Debostuti Ghosh Dastidar
> Department of Biotechnology
> Indian Institute of Technology Madras
> _______________________________________________
> 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 Mon Sep 01 2014 - 08:30:02 PDT
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