Re: [AMBER] contacts with water

From: Daniel Roe <>
Date: Fri, 2 Jan 2015 11:54:23 -0700


The 'nativecontacts' command by default excludes solvent - you need to
use the 'includesolvent' keyword to include it. If the calcium ion is
not covalently bound you could also try using the 'hbond' command with
the 'solventdonor' and 'solventacceptor' keywords pointing towards
your water, and the 'nointramol' keyword to ignore intramolecular
hydrogen bonds.

Hope this helps,


On Thu, Jan 1, 2015 at 9:51 PM, Chinthaka Ratnaweera <> wrote:
> Hi
> I want to determine the interactions of a coordinated metal ion (Ca) in a
> protein during a MD simulation. Through visualization of the trajectory I
> noted that water molecules are also a part of the coordination sphere. I
> tried to find the contacts with nativecontacts and contact commands in
> cpptraj but it gives only the contacts with protein but not the water
> molecules. (says nothing selected for ':WAT')
> Is there a way I can find all the contacts including those with water?
> Thank you
> Chinthaka
> _______________________________________________
> 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 Jan 02 2015 - 11:00:03 PST
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