AMBER Archive (2003)

Subject: mm_pbsa

From: Layi Adekoya (adekoya_at_fagmed.uit.no)
Date: Wed Feb 26 2003 - 04:05:35 CST

Hi,
I have a question on MM_PBSA/GBSA.
After MD simulation of the
receptor, receptor complex and ligand in water.
One removes the water and ions from the snapshots.
The elctrostatic contribution is calculated either
using PB or GB.
my question is which will be more accurate
GB or PB since we removed the solvent before running the script mmpbsa.in?
Will it matter if one had water in the MD simulation but
calculated elctrostatic contribution using
GB alone for MM_GBSA?

Thanks in advance.

Layi