On Sat, Apr 28, 2012, Jesper Sørensen wrote:
>
> 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.
You can of course use any set of radii you like, or that you wish to try out.
In my experience, the bondi radii (or their modified variants) work fairly
well. You can use "optimized" radii (such as SWANSON) and see how much
difference it makes. You can even use the LJ radii (not sure if these are
sigma or rmin). There is no single "right" answer; some programs try to
guide the user towards a recommended set; others try to provide maximum
flexibility.
>
> 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).
Depends on the radiopt parameter; when radiopt=0, it uses whatever radii are in
the prmtop file.
....dac
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Received on Sat Apr 28 2012 - 19:30:03 PDT
