[AMBER] how to decide water mediated interaction betwen

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Mon, 28 Feb 2011 10:14:31 +0530 (IST)

Hello all

I have one question regarding H-Bond calculation as I have to find out water
mediated H-Bond betwen
protein and DNA during MD simulation.
I have included solventneighbor, solventdonor, solventacceptor in command:

hbond solventneighbor 9 solventdonor WAT O solventacceptor WAT O H1
solventacceptor WAT O H2 time 2 print .05 series hbt

It is giving interaction betwen:

 solventdonor WAT O
 solventacceptor WAT O H1
 solventacceptor WAT O H2


 either protein or DNA

Here how I can decide that interacting residues of protein and DNA those
interacting with water actually interacting with each other like in crystal
structure i.e. water mediated interaction.

Sangita Kachhap

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Received on Sun Feb 27 2011 - 21:00:02 PST
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