Dear Sir,
Thanks once again.
Silver
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Tuesday, January 20, 2015 1:49 PM
To: AMBER Mailing List
Subject: Re: [AMBER] HBond ANALYSIS
Hi,
On Tue, Jan 20, 2015 at 12:36 PM, Sylvester Tumusiime <stumusii.uno.edu> wrote:
> 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
Actually you want just the opposite. The intent of the 'solventdonor'
and 'solventacceptor' keywords is to track "non-specific" hydrogen
bonds, i.e. we only care what the identity of one of the partners is
(the solute). So you can just specify K+ as your "solvent":
hbond HBONDWat1 out HBONDWat-N1.dat :1 angle 135 dist 3.0 series \
solventdonor :K+ solventacceptor :K+ solvout SOLVOUTWat1.dat
-Dan
>
> 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
>> _______________________________________________
>> AMBER mailing list
>> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> 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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jan 20 2015 - 13:00:02 PST
