Re: [AMBER] MMPBSA question

From: Jason Swails <>
Date: Sat, 19 Mar 2011 17:31:02 -0700


My comments are below:

On Sat, Mar 19, 2011 at 4:35 PM, Eliac Brown <> wrote:

> Dear AMBER
> I have been reading on MMPBSA and different methodologies for SASA
> calculation.
> As I am aware, reads the radii from the prmtop file, but the
> written radii in the prmtop file is the effective born radii, and this is
> different from the vdw radii which is needed in ICOSA calculation (after

This is not quite accurate. Effective Born radii are recalculated
throughout the simulation (every step unless you specify nrespa != 1).
These are calculated via the coloumb field approximation, generally, which
involves integrating over the volume of all other atoms. The radii stored
in the prmtop file is *that* radius. While it's true that they are
optimized for different GB models, they are not very far off of the VDW

augmentation by 1.4 for the solvent probe). So, how it comes?
> On the other hand, using version, ICOSA reads the radii from
> compiled mdread file, but when I check the defined radii for chlorine in
> mdread, I couldn't find it, and the program didn't complain, why? in other
> case it complains such as in the case of zinc.
> Any clarification would be appreciated.

If you look at line 1806 of mdread.f, you'll see that (for gbsa=1), the
default atomic radii are set as 1.70 + the solvent probe radius (which is
why you didn't get an error).

Hope this clarifies things,

Thanks in advance
> Eliac
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Sat Mar 19 2011 - 18:00:03 PDT
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