From: Jason Swails <>
Date: Tue, 20 Dec 2011 16:21:56 -0500

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.


On Tue, Dec 20, 2011 at 8:41 AM, Toshifumi Yui <>wrote:

> As working with tutorial 3 of MM_PBSA, I found the following message in the
> 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
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Tue Dec 20 2011 - 13:30:03 PST
Custom Search