[AMBER] AMBER11 MMPBSA.py tutorial section 3.6

From: <Yokota_Akihiro.takeda.co.jp>
Date: Mon, 7 Feb 2011 16:54:11 +0900

Dear AMBER users,

  I have a question about "Polar Solvation" energy for each residue in MMPBSA.py tutorial section 3.6.
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.htm

  In the middle of the file below, there is a comment "Energy Decomposition Analysis (All units kcal/mol):
Poisson Boltzmann solvent", I think this means that "Polar Solvation(PB)" of "each residue" can be calculated.
http://ambermd.org/tutorials/advanced/tutorial3/py_script/files/FINAL_DECOMP_MMPBSA_perres.dat

However PB energy cannot be decomposed straightly by the definition (On the other hand, GB energies can be decomposed).
Does anyone teach me how the PB energies are decomposed into each residue?

Thanks in advance,
Akihiro Yokota

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Received on Mon Feb 07 2011 - 00:00:04 PST