Re: [AMBER] request for help

From: Daniel Roe <>
Date: Sat, 11 Jan 2014 17:14:33 -0700


First, I recommend you update to the latest version of cpptraj, 13.22. You
can update your entire AmberTools distribution by re-running configure,
then re-compiling.

To track hydrogen bonds you can use the 'hbond' command of cpptraj. First,
ensure your methanol residues are marked as solvent by using the 'solvent'
command. Then use the 'hbond' command with the 'acceptormask' set to the
oxygen of your organic molecule and the 'solventdonor' mask set to
methanol. You can then get the total number of solute-solvent hydrogen
bonds formed in the file specified by the 'out' keyword. For example, say
your organic residue is named MOL, the oxygen atom is named O, and your
methanol residues are named MOH:

hbond acceptormask :MOL.O solventdonor :MOH out numhb_v_time.agr solvout

Note in the above example 'numhb_v_time.agr' will be written in xmgrace

Hope this helps,


On Sat, Jan 11, 2014 at 1:54 AM, Robin Jain <>wrote:

> Dear sir,
> I am solvating a organic molecule in methanol. Now i have some problem for
> which i want your help.
> I want to know that in which frame the oxygen atom of organic molecule
> formed zero, one and two hydrogen bond with methanol hydrogen. I am using
> cpptraj version 13.0.
> Please help me in this regard.
> --
> Robin Jain
> _______________________________________________
> AMBER mailing list

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)
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Received on Sat Jan 11 2014 - 16:30:02 PST
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