[AMBER] PBSA sprob question

From: Jesper Sørensen <jesorensen.ucsd.edu>
Date: Tue, 13 Mar 2012 13:49:09 -0700

Hi all,

I have been trying to understand the EPB value in terms of different surface definitions, the vdW or SE.

To change the surface definition I have used the dprob variable.
For vdW dprob=0
for SE dprob=1.4

My question is now what should the sprob value be and what does it affect?
In the AmberTools 1.5 manual it states that the sprob value is (in this version) is used to calculate the dispersion term and potentially also the cavity term.
Neither of these values should be part of the EPB value, correct?

I've done some tests...

                dprob sprob EPB
A 0 0 191 kcal/mol
B 0 1.4 234 kcal/mol
C 1.4 1.4 234 kcal/mol
D 1.4 - 234 kcal/mol
E 0 - 239 kcal/mol

In D and E I have let sprob be undefined, which means it should go back to default values. In the log file I cannot see what that default value is, but apparently it is not 0 (zero) or 1.4 in the case of the dprob=0, when you compare A, B and E.
When dprob=1.4, it seems likely that sprob could default to 1.4, when comparing C and D, but I am not sure this is true.
Again, should sprob even affect the EPB value?

I hope you can help me understand this parameter better.

Best regards,

AMBER mailing list
Received on Tue Mar 13 2012 - 14:00:03 PDT
Custom Search