Hi,
On Tue, Jul 8, 2014 at 12:55 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>
> I am interested in analysing solute-solvent interactions (not bridging
> interactions). Is there a way to print the solvent residue number in the
> output rather than printing just solventdonor and solventacceptor?
>
Yes this is possible by explicitly specifying donors and acceptors with the
'donormask' and 'acceptormask' keywords respectively and using the
'nointramol' keyword to ignore intramolecular hydrogen bonds, e.g.:
hbond hb donormask * acceptormask * nointramol out solvhb.dat avgout
solvavg.dat
Be aware that this is going to generate a TON of data since you will be
getting water-water hydrogen bonds as well. You could potentially reduce
this noise by running a 'closest' command prior to the 'hbond' command and
keeping only the first shell of waters (determined with 'watershell').
Hope this helps,
-Dan
>
> Many thanks,
> Neha
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Curtin Research Fellow,
> School of Biomedical Sciences,
> Curtin University,
> Perth GPO U1987
> Australia
> LinkedIn
> Research Gate
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 Jul 08 2014 - 13:00:02 PDT
