Re: [AMBER] Radii in prmtop

From: Jesper Sørensen <>
Date: Sat, 28 Apr 2012 14:38:30 -0700

Hi Dave,

Thanks for the reply. Perhaps you can clarify something for me in this regard.
PBSA, DELPHI and APBS all look for "intrinsic electrostatic radii" as you called it.

Using a prmtop from amber and converting it to a pqr file using ambpdb, this will result in the radii being mbondi2 (or similiar) like in my previous example.
Are these really the radii that one should use for PB electrostatics calculations? Shouldn't it be the vdW radii from the force field? mbondi-variations were developed for GB calculations for the most part weren't they?

In terms for APBS, you can supply pdb2pqr with a PDB file and it will return a pqr file with different radii, which can also be used for electrostatics calculations.
It will return PARSE, SWANSON, TYL06, PEOEPB, or AMBER (94). Which were all developed for for PB calculations using specific parameters.
Now when you ask it to return AMBER you actually get the FF radii and not the "intrinsic electrostatic radii", like leap/ambpdb returns. So APBS will actually use the vdW radii.

What does PBSA do when you supply it with a prmtop file? Use the vdW radii or the "intrinsic electrostatic radii" (unless of course you ask it for TYL06 radii).

I realize that this may be a topic, which is being debated quite a bit in literature, but I'd appreciate your (or anyone else on the lists) perspective on this.

Best regards,

On Apr 26, 2012, at 6:46 PM, case wrote:

> On Thu, Apr 26, 2012, Jesper Sørensen wrote:
>> Thanks, I found those flags now.
>> The reason I ask is that when you use ambpdb to write out a PQR file -
>> to use with delphi or APBS, that prints out data from (%FLAG RADII),
>> which is what confused me in the first place - as the radii were not
>> what I expected them to be.
> That is because delphi and APBS are electrostatic programs, looking for what
> is most precisely called the intrinsic electrostatic radii, and just called
> "RADII" in the prmtop file. I agree that a better name for that section could
> have been chosen.
> ...dac
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Received on Sat Apr 28 2012 - 15:00:02 PDT
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