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
