On Mon, Jul 26, 2010, Asfa Ali wrote:
>
> I need to add the radius of K+ ions in mm_pbsa_calceneent.pm file which
> does not contain the information for K+ ion :
>
> "N" => 1.550 + 1.400,
> "H" => 1.200 + 1.400,
> "C" => 1.700 + 1.400,
> "O" => 1.500 + 1.400,
> "P" => 1.800 + 1.400,
> "S" => 1.800 + 1.400,
> "FE" => 1.300 + 1.400,
> "Na+" => 1.200 + 1.400,
> "Cl-" => 1.700 + 1.400,
> "MG" => 1.180 + 1.400,
>
> Can anyone tell me the radius of K+ ion so that I can add it here ?
This was just discussed a couple of days ago:
http://archive.ambermd.org/201007/0538.html
Two notes:
(1) please don't confuse "dielectric radii" used in continuum solvent
models with Lennard-Jones radii used in explicit solvent calculations.
(2) Using explicit ions in MM-PBSA calculations is a *very* advanced topic,
not supported by default in Amber. My best advice is "don't do it". If you
really want to try, you'll have to figure out how to do it, and what
parameters to use, on your own. At that point, you can answer questions on
the mailing list, instead of asking them :-)
....dac
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Received on Mon Jul 26 2010 - 05:00:05 PDT
