[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

  and

 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
JRF
BIC,IMTECH
CHANDIGARH


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