Thank you Dan.
On Jul 9, 2014 3:33 AM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> 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 Wed Jul 09 2014 - 08:00:02 PDT
