Dear sir,
Thank you for your suggestions, they have been tremendously helpful.
Regarding your question: Why do you have residue 1 (:1) as your solvent acceptor? Is it solvent, or solute? The answer is that it is my solute. So now i understand your layout of your command.
Supposing i was considering hydrogen bonding between an ion (K+) and my residue (:1), am guessing that it would make best sense in this instance to consider my molecule/residue as the solvent and the ion as my solute to give this as a possible command:
hbond HBONDWat1 out HBONDWat-N1.dat :K+ angle 135 dist 3.0 series \
solventdonor :1 solventacceptor :1 solvout SOLVOUTWat1.dat
thank you very much,
Silver
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Tuesday, January 20, 2015 12:04 PM
To: AMBER Mailing List
Subject: Re: [AMBER] HBond ANALYSIS
Hi,
On Sun, Jan 18, 2015 at 10:44 PM, Sylvester Tumusiime <stumusii.uno.edu> 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,
-Dan
> Thank you,
> sincerely,
> Silver
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jan 20 2015 - 12:00:03 PST
