From: Daniel Roe <>
Date: Tue, 20 Jan 2015 11:04:52 -0700


On Sun, Jan 18, 2015 at 10:44 PM, Sylvester Tumusiime <> wrote:
> 1. I have noticed that when i have autoimage or not, i get different results
> in the SOLVOUTWAT.dat file (see commands below). I am wondering whether or
> not it is important to include autoimage in my commands. This is my setup:

If you're interested in hydrogen bonds between molecules (such as
between solute and solvent) then 'autoimage' is very important, since
the distance/angle calculations in 'hbond' are not themselves imaged.

> hbond HBONDWat1 out HBONDWat-N1.dat :1 angle 135 dist 3.0 series
> solventdonor :WAT solventacceptor :1 solvout SOLVOUTWat1.dat
> 2. Is it possible to have a look at my set up above and let me know if the
> hbond command is correct. I have noticed that in some instances, the
> SOLVOUTWAT.dat file is empty while in others its not. I read that i can
> substitute water with ions as the solventdonor. I plan to use the above set
> up and am wondering if this would be okay.

Why do you have residue 1 (:1) as your solvent acceptor? Is it
solvent, or solute? If you're looking for hydrogen bonds between
solvent and solute residue 1, you want something like:

hbond HBONDWat1 out HBONDWat-N1.dat :1 angle 135 dist 3.0 series \
  solventdonor :WAT solventacceptor :WAT.O solvout SOLVOUTWat1.dat

> 3. Is the placement of the solvent donor and solventacceptor keywords
> acceptable?

The placement of these keywords does not matter as long as they are
followed by a valid atom mask expression.

Hope this helps,


> Thank you,
> sincerely,
> Silver
> _______________________________________________
> 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 Tue Jan 20 2015 - 10:30:02 PST
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