Sir,
Thank you so much for the reply.
I do not have cpptraj. Can the same be accomplished with ptraj ?
On Tue, Dec 31, 2013 at 9:28 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Asfa Ali
Prof. S. Bhattacharya's group,
Dept. of Organic Chemistry,
Indian Institute of Science,
Bangalore-12
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Received on Wed Jan 01 2014 - 06:30:02 PST
