Henry,
1. You can check the saved files, both input and output for pbsa to
see whether the keyword gets set according to your python input file.
2. The default boundary condition in pbsa is indeed the same as that
in Delphi. However, there is an additional keyword needed to reproduce
the Delphi energy. I think it is smoothopt = 2.
3. If you want an easier control in the comparison, turn off focusing
in both programs.
The analysis of all these related issues can be found in
J. Wang, Q. Cai, X. Ye, and R. Luo, Reducing Grid-Dependence in
Finite-Difference Poisson-Boltzmann Calculations, J. Chem. Theo.
Comp., 8:2741–2751, 2012.
All the best,
Ray
On Sat, Dec 8, 2012 at 11:02 AM, <psu4.uic.edu> wrote:
> Dear amber developers,
>
> We are currently using MMPBSA.py.MPI to compare the results with Delphi.
> The following is the setting we use:
>
> Input file for running PB
>
> &general
>
> keep_files=2,
>
> /
>
> &pb
>
> istrng=0.150, fillratio = 2.0,
>
> /
>
>
>
> Here are two questions:
>
>
> 1. In Amber PBSA, we are allowed to set IPB to 1 to make sure pbsa is using
> the exactly same surface defination as Delphi. Since we are not aware any
> adjustable IPB related setting in MMPBSA.py.MPI, may we know if we are able
> to set IPB related setting in MMPBSA.py.MPI? Or the default setting of IPB
> is 1 in MMPBSA.py?
>
>
> 2. Also, Delphi sets the boundary condition by bndcon=4 and Amber “pbsa”
> sets the boundary condition as BCOPT = 5. So are the boundary condition
> setting in MMPBSA.py.MPI the same as in Delphi?
>
>
>
> Best,
>
> Henry
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Received on Sat Dec 08 2012 - 16:00:02 PST
