Dear Dubey and Roe,
Thanks for your immediate reply.
Anu
On Tue, Aug 13, 2013 at 7:54 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> The 'hbond' command in cpptraj will do what you want. Right now
> probably the best way to look at only inter-molecular hydrogen bonds
> is to use two separate 'hbond' commands: one where you define ligand
> donors and protein receptors, and the other where you define ligand
> receptors and protein donors (e.g. using the 'donormask' and
> 'acceptormask' keywords).
>
> Hope this helps,
>
> -Dan
>
> On Tue, Aug 13, 2013 at 12:37 AM, anu chandra <anu80125.gmail.com> wrote:
> > Dear Amber users,
> >
> > I am working with protein-ligand interaction. I would like to see the
> > number of hydrogen bonds ligand make with protein along the simulation
> > trajectories. Is there a tool in PTRAJ/CPPTRAJ to do such a calculation?.
> > Waiting for your valuble reply.
> >
> >
> > Thanks in advance
> >
> > Regards,
> > Anu.
> > _______________________________________________
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> > 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) 585-9119 (Fax)
>
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>
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Received on Tue Aug 13 2013 - 23:30:10 PDT
