Hi,
On Mon, Dec 30, 2013 at 2:43 PM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> However, I would also like to know the presence of H-bonding between ligand
> and DNA/RNA bases. Can anyone tell me whether that is possible and if so,
> how ?
>
You can do this in cpptraj using the 'hbond' command with the 'nointramol'
keyword, which tells the command to ignore intramolecular hydrogen bonds.
You need to use cpptraj from AmberTools 13 with all updates applied. For
example:
hbond nointramol out numhbvtime.dat avgout hbavg.out
Note that the 'hbond' command has different syntax in cpptraj than it did
in ptraj; see the manual for more details.
-Dan
>
> Thanks in advance
> Asfa
>
> --
> Asfa Ali
> Prof. S. Bhattacharya's group,
> Dept. of Organic Chemistry,
> Indian Institute of Science,
> Bangalore-12
> _______________________________________________
> 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 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 Dec 31 2013 - 08:00:02 PST
