Hello,
I do MMPBSA per-residue decomposition for a receptor-ligand system (with
MMPBSA.py from AT 1.5) and am wondering how the numbers in the Polar
Solvation column in FINAL_DECOMP_MMPBSA.dat have actually been built.
I understand the PB part of PBSA for a system comprised of a low
dielectric volume containing some charge distribution placed in a high
dielectric medium. Now, what is done to consider the contribution of
only a single residue of the system?
Considering the contribution of residue R: is the volume of the low
dielectric medium still defined by all atoms (i.e. entire receptor or
ligand or receptor+ligand) while the atomic charges of all residues
except for R are considered to be zero?
I would be happy to get some insights!
Cheers,
Jan-Philip
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Received on Wed Jul 25 2012 - 03:30:03 PDT
