Dear apbs-users,


I have been trying to run the HEWL Glu 35 calculations as discussed on the APBS tutorial, to

this end I have, using the input file given in the tutorial and setting the 2LZT-GLU35.pqr as

the ref.pqr obtained the following values:


2LZT-GLU35.out = 1.131872537865E+04 kJ/mol

2LZT-noGLU35.out = 1.122562184449E+04 kJ/mol

GLU35.out = 1.035980096096E+02 kJ/mol


2LZT-GLH35.out = 1.132973544557E+04 kJ/mol

2LZT-noGLH35.out = 1.122564525883E+04 kJ/mol

GLH35.out = 1.087438847994E+02 kJ/mol


Combining these value should, I believe, allow me to calculate the pKa shift as follows :


(2LZT-GLU35.out - 2LZT-noGLU35.out - GLU35.out) - (2LZT-GLH35.out - 2LZT-noGLH35.out - GLH35.out) =

(11,318.7 kJ/mol - 11,225.6 kJ/mol - 103.6 kJ/mol ) - (11,329.7 kJ/mol - 11,225.6 kJ/mol - 108.7 kJ/mol) =


                    (-10.494 kJ/mol)                                        -                                  (-4.654 kJ/mol)                                = -5.840 kJ/mol

and so

pKa shift = deltaG/(2.303*R*T) = (-5840)/(2.303*R*T) = -1.0


Now using a model Glu value of pKa 4.4 gives me a pKa for Glu 35 of 3.4


I know that the answer I obtain is incorrect as both PROPKA and literature experimental values give a pKa of ~ 6,

what I do not know is whether this is due to an error in my understanding of the calculation or in the input file

used (I've also tested using various modification of the input files but all to no avail: a dime of 257 257 257; an Amber

forcefield and different pdies ) or even an inability of the code to produce a correct result.


All tips, hints, insights (sign errors etc.) and answers graciously accepted.


Apologies if I have made some annoyingly elementary error but I am stuck.


Regards


Charlie