Dear Amber users,
I am working with a dimeric protein system and I am trying to calculate
the binding free energy change between two monomeric units in presence and
absence of bound ligand, using MMPBSA.py. Though the calculation finished
successfully, I find a huge difference between the GB and PB deltaG values
for the same system.
In presnce of ligand, the GB value is -67.17 and the calculate PB value
for the same system is -675.37. Similarly, in absence of ligand, the GB
value is -82.54 and the calculate PB value for the same system is -810.19.
As expected, though the GB and PB values maintain the trend ( ie. low
binding free energy in presence of ligand) I just wonder that such a high
PB values are safe to report?
I have following input for GB abd PB calculations,
********************************************************************************
Input file for running PB and GB
&general
startframe=1, endframe=1250, interval=20, verbose=1,
keep_files=0,search_path=1,
/
&gb
igb=8, saltcon=0.100,
/
&pb
istrng=0.100, inp=1, radiopt=0,
/
***********************************************************************************
Many thanks in Advance
Anu
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Received on Wed Dec 02 2015 - 06:00:11 PST
