Dear all,
I am now trying to use the pbsa module in AMBER11 to calculate the binding
free energy between a protein and a ligand.
I have a question on the choice of the values for SURFTEN/SURFOFF.
I read the AMBER manual on mm_pbsa and tried the test example. The following
are the descriptions for the two parameters both in the manual and in the
input file for mm_pbsa calculations in the test example.
# SURFTEN/SURFOFF - Values used to compute the nonpolar
# solvation free energy Gnp acccording to INP.
# If INP = 1 and RADIOPT = 0 (default, see above),
# use SURFTEN/SURFOFF parameters that fit with the radii from the
# prmtop file, e.g., use SURFTEN: 0.00542; SURFOFF: 0.92 for PARSE
radii.
# Otherwise, please
# set these to the following: SURFTEN: 0.04356; OFFSET: -1.008
It states clearly that If INP = 2 and RADIOPT = 1, these two lines can be
removed, i.e. use the default values set in pbsa for this nonpolar solvation
model.
So I set INP = 2 and RADIOPT = 1, and commented the two lines for both
SURFTEN and SURFOFF. From the output file I found SURFTEN=1.0000 and
SURFOFF=0.000.
However, in the test example (03_MMPBSA_Binding), when INP = 2 and RADIOPT =
1, SURFTEN and OFFSET are set to be 0.04356 and -1.008, respectively.
My question is when INP = 2 and RADIOPT = 1, what are exact values for
SURFTEN and SURFOFF please？
Any suggestions and help would be greatly appreciated!
Many thanks!
Qiong Zhang
Department of Theoretical Chemistry & Biology
School of Biotechnology
Royal Institute of Technology
Roslagstullsbacken 15
SE-10691 Stockholm, Sweden
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Received on Sat Oct 22 2011 - 14:00:03 PDT
