Re: [AMBER] MMPBSA warning

From: Jason Swails <>
Date: Fri, 18 Jun 2010 09:09:18 -0400

Hi George,

Like you pointed out, this is not a fatal warning. It would have been a
fatal warning if not all of your prmtop files were created with the same PB
Radii set (if this were the case, your results would have been
meaningless!). In my experience, mbondi and mbondi2 radiis are similar,
though not identical. Each GB model was parameterized with a specific
radius set, which is why that radius set is suggested for use with that gb

This is not a flag in the MMPBSA calculation, but rather a parameter set in
leap when you create the prmtop files. See the command

set default pbradii _______

in leap. The default is mbondi, so if you didn't specify one, that's why it
is mbondi. Specifying mbondi2 will get rid of this warning. You can re-run
a couple of frames using mbondi2 and compare the results obtained from
mbondi if you would like, but because mbondi and mbondi2 are similar, and
the delta G is calculated as a difference, I'm guessing the effect in this
case will be minimal.

Hope this helps,

On Fri, Jun 18, 2010 at 6:54 AM, George Tzotzos <> wrote:

> Hi everybody,
> I got the following warning during my binding affinity calculation, which
> terminated successfully
> igb=2 should be used with mbondi2 pbradii set. Yours are modified Bondi
> radii (mbondi)
> I'd appreciate if anyone could enlighten me on the significance of this
> warning and which is the right flag to use for modified Bondi raddii
> Regards
> George
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Jun 18 2010 - 06:30:09 PDT
Custom Search