AMBER Archive (2004)

Subject: Re: AMBER: PBCAL in MM/PBSA

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Fri Jun 25 2004 - 14:37:07 CDT

Hi,

if you know, or can at least guess the solvation free energy your ligand
should have, you can experiment with charges until you get the correct PB
result for the free ligand and then apply these charges to the MMPBSA
calculation

> I am using mm/pbsa to calculate bind energy of protein+ligand complex.
Delphi is used to calculate PB value. My question is: Is there any
recommendation or preference of which type of charge should be assiged to
ligand (I use amber94 for protein) since I found a huge difference of
PBCAL value of ligand(~10 kcal) comparing the results from gasteiger
charge(for ligand) and AM1 charge(for ligand). Does anyone has the
similiar experience? Your suggestion will be highly appreciated!

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