Hello all
I want to study the effect of perticular water molecule on affinity and specificity
of protien DNA binding.
As these can be define by standared free energy change I thought,if I can
calculate the
standared free energy change of protein - DNA interaction
1)considering that perticular water molecule in interaction
2)In absence of that perticular water molecule
Then the effect of water molecule in affinty and specificity can be define.
So I thought to use MMPBSA but it runs implicit and I am not getting how to include
that perticular water molecule in calculation of standared free energy change.
Can anyone please suggest is it possible and how to do it?
With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Fri Feb 04 2011 - 23:30:05 PST
