Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...

From: Ray Luo, Ph.D. <>
Date: Tue, 7 Aug 2012 15:15:38 -0700

On Tue, Aug 7, 2012 at 6:53 AM, Vlad Cojocaru
<> wrote:
> However, one mistery remains. Why using inp=2 and radiopt=0 still gives
> the same error but inp=1 and radiopt=0 does not ? As far as I got it,
> radiopt=0 should force to read radii from the topology file and
> therefore in should work with any inp value. Or maybe when setting inp=2
> the program overwrites automatically the radiopt=0 from the input file ?

Just to clarify a few things here. inp=1 instructs PBSA to use a
single term linearly proportional to the molecular surface for the
nonpolar solvation free energy, so it is compatible with radiopt=0,
i.e. an end user can do whatever he/she wants with the radii and
surface tension/offset etc from the input files and prmtop files.

When setting inp=2, you are asking PBSA to use the manually optimized
radii (with respect to TIP3P) for nonpolar solvation free energy.
Doing so apparently contradicts with the intention of setting
radiop=0, i.e. using the modified Bondi radii in the prmtop file. So
far these radii are hand coded inside PBSA. That's why Jason suggested
you to look at the code.

Ideally, these should be provided in a data file along with the Amber
force field and to be written into the future generations of prmtop
files by Leap. As Jason mentioned in his email, we are also lagging
behind in optimizing radii for all the available atom types/force
fields in Amber. Nevertheless, we are putting these tasks on the top
of the TODO list for the next release cycle.


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Received on Tue Aug 07 2012 - 15:30:02 PDT
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