Hello,
I am new to the field and after reading quite some literature about
MMPBSA, I am still wondering about the specific step of calculating the
coulomb energy of the solvent within the electrostatic potential PHI(r)
caused by the charge distribution of the solute rho(r).
I understand that by solving the PBE with rho(r) as input, we get
PHI(r). Now, we want to know (at least in my picture of the things) the
sum of the electrostatic energies of all solvent molecules placed into
this potential. Is that correct so far? This would be some
method/function taking PHI(r) and solvent properties as input and
providing the energy as output.
As implicit solvent models are used, I doubt that we simply sum up the
coulomb energy of the partial charges of all solvent molecules within
PHI(r) (what would be wrong with this approach, by the way?).
This step was left unexplained in each paper I've read. If you have a
good reference for this, I would be very happy to read it. And if it is
so obvious that it is not worth explaining it in one of the basic
papers, then I would be happy to know what the obvious is :)
I think "the secret" is behind this sentence of the AmberTools manual:
"The charging free energy is a function of the electrostatic potential PHI".
It suggests that the problem is solved from the perspective of
calculating the system's free energy change while "charging" the solute,
but it also does not explain the details and does not give a reference.
Hope that someone can help me out here.. thanks a lot!
Jan-Philip
--
Jan-Philip Gehrcke
PhD student
Structural Bioinformatics Group
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
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Received on Wed Aug 10 2011 - 05:00:02 PDT
