Hi,
Check out the 'hbond' command in cpptraj - this can be combined with
the 'lifetime' command to perform lifetime analysis. Examples are
given in the manual. Also check out this tutorial:
http://www.amber.utah.edu/AMBER-workshop/London-2015/Hbond/
Hope this helps,
-Dan
On Fri, Apr 29, 2016 at 7:27 AM, Jag Silwal <jagsilwal.gmail.com> wrote:
> Dear all,
>
> Could somebody give me some detail explanation on calculating
> residue-specific values for percentage hydrogen bond lifetimes during MD
> Simulation? I have a protein-protein complex and I want to calculate the
> percentage of intermolecular hydrogen bonds observed during the MD
> simulation of the complex.
>
>
> Thanks for your time in advance.
>
> Jag
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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 Fri Apr 29 2016 - 08:30:04 PDT
