Dear all,
We are going to calculate the binding free energy between a protein and its ligand by MMPBSA module in AMBER10.
I'd like to know how to set the dielectric constant in NMODE calculation.
In this case, is the electrostatic energy calculated by 1/(4*PI*(DIELC*R)*R)?
The default value in amber is 1.0, whereas a value of 4.0 is used in the example script (mm_pbsa.in) in AMBER manual.
Which one should I use?
Many thanks.
Best Regards.
J. Yang
2010-02-04
-----------------------------------------------
State Key Lab of Molecular Reaction Dynamics (SKLMRD),
Dalian Institute of Chemical Physics(DICP),
the Chinese Academy of Sciences(CAS),
Zhongshan Road457, Dalian City,
Liaoning Province 116023,P. R. China
E-mail:
mjyang.dicp.ac.cn
Office Phone:
+86+411+84379352
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Received on Wed Feb 03 2010 - 19:00:02 PST
