From: Jason Swails <>
Date: Fri, 4 Jul 2014 12:04:41 -0700

On Fri, Jul 4, 2014 at 2:10 AM, Sourav Purohit <> wrote:

> While setting up simulation for a complex, I did not set default PBRadii to
> mbondi2. Now I plan to perform MMPBSA calculation for the complex. Will I
> get wrong results if i use igb=2 ?

​You should set your radii to the recommended set for the GB value. Energy
differences with GB can be quite sensitive to small changes in intrinsic
radii (this sensitivity is especially enhanced when the net charge changes,
like with pKa calculations).

You can use ParmEd to change the solvent radii without having to go through
tleap again. Something like this: -p <your.prmtop> << EOF
changeRadii mbondi2
parmout new.prmtop

Alternatively, you can use if you prefer a GUI​ that you can
click with. In this case, just running "" will bring up a file
browser, or " <file>" will bring up the action window where you
can modify your topology file. More information here:


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Jul 04 2014 - 12:30:02 PDT
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