Hi,
On Tue, Mar 28, 2017 at 5:24 AM, Ming Tang <m21.tang.qut.edu.au> wrote:
> Is there a way to get the water bridge percentage during MD simulations between two specific atoms at two specific residues?
Sure. Use the cpptraj 'hbond' command, specify the two residues of
interest, the 'solventacceptor'/'solventdonor' keywords, and the
'bridgeout' keyword. For example, to see how many frames residues 5
and 12 were bridged by water:
hbond HB :5,12 solventacceptor :WAT.O solventdonor :WAT bridgeout solvavg.dat
Note that this will give you the number of frames, but it is
straightforward to convert that to a percentage. See the Amber 16
manual for full details on those keywords plus additional keywords for
the 'hbond' command.
-Dan
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Mar 28 2017 - 06:30:03 PDT
