Dear Qiong,
May I suggest you to use the Ambertool release for your calculation so
you may have a better control of all the input parameters, i.e. by
following the manual suggested values? The perl scripts (including its
comments) haven't been updated for a while ...
All the best,
Ray
On Sat, Oct 22, 2011 at 1:56 PM, Qiong Zhang <qiong.zhang.qzh.gmail.com> wrote:
> 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 - 21:30:03 PDT
