You should typically use the radius set that the GB model was parametrized
with. Therefore, I would make sure to generate topology files with the
appropriate radius set if you were trying to use your results for some kind
of publication.
It's OK for a demonstration and probably more important for dynamics to use
the correct radii, but it's generally good practice to use parameters that
were designed together.
I also recommend you use tleap when generating your topologies, as I've had
problems with sleap in the past setting the GB radii correctly.
HTH,
Jason
On Tue, Dec 20, 2011 at 8:41 AM, Toshifumi Yui <tyui.cc.miyazaki-u.ac.jp>wrote:
> As working with tutorial 3 of MM_PBSA, I found the following message in the
> FINAL_RESULTS_MMPBSA.dat file.
>
> WARNINGS:
> igb=2 should be used with mbondi2 pbradii set.....
>
> So I have carried out another trial calculations using a set of trmtop
> files
> created with "set default PBradii mbondi2" command, which gave different
> energy values for both GB and PB methods.
> Also I've got the same message again in the FINAL_RESULTS_MMPBSA.dat file
> produced by the trial calculations.
>
> I wonder that I don't have to worry about this warning any way, and is this
> Ok to use the trmtop files based on the normal PBradii setting according to
> the tutorial, even using igb = 2 option ?
> I am very confusing.
>
> Thank you
>
> Regards.
>
> Toshi Yui
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Dec 20 2011 - 13:30:03 PST
