Hi Jason
I was successful in reproducing the CpHMD simulations for the HEWL protein
and moved on to a non protein system. I chose the Succinic Acid system (
COOHCH2CH2COOH) performed a Thermodynamic Integration. The delta G obtained
was + 32 kcal/mol which was really strange as this compound has a pKa of
4.2. I abstracted a proton from only one of the COOH groups. When I used
this value for CpHMD in AMBER , I got a 50% protonation at pH = pKa. I know
the del G is totally off as this is a acid and it would like to dissociate
as a result giving a negative del G. I checked the pKa and del G values of
Aspartic and Glutamic Acid . Aspartic Acid has a pKa of 4 and a del G value
of -26 kcal/mol and Glutamic Acid has a pKa of 4.4 and del G value of -8
kcal/mol (data obtained from residues.py). I expected the del G value of
Succinic acid to be in between these two values.
Do you have an idea about why a positive value of del G is obtained in this
case and CpHMD working fine for a wrong value of del G
Thank You
Rahul Ramesh
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Received on Fri Sep 11 2015 - 18:30:03 PDT
