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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--
-------------------------
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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Received on Tue Aug 13 2013 - 07:30:01 PDT
