Re: AMBER: No radius found for K+ (MM_PBSA)

From: Thomas Cheatham III <>
Date: Fri, 21 Dec 2007 11:53:55 -0700 (Mountain Standard Time)

> I am trying to calculate absolute free energy for the nucleotide
> molecule using MM_PBSA script of AMBER8. The system has some K+ ions in
> the active site. I wish to calculate the absolute free energy in
> presence of these ions.
> Shall I include the radius in "" file or any other
> file? If yes please let me know the accurate value of radius for K+ ion.

What we have done in the past is to create a single ion system (of K+) and
run this through MM-PBSA to see what the calculated solvation free energy
would be. Then we alter the radii of the K+ until an accurate free energy
of solvation is obtained using the continuum model. Valid target values
can be found in papers by Schmid et al. and/or Marcus et al. (although
we've had better success with the former). This was discussed briefly in
the Stefl et al. (2003) Biophys. J. 85, 1787-1804 article where this
procedure was done for Na+. We have not tried to find the appropriate
radii for K+.

> Shall I recompile the AMBER after addition of these values?

Recompiling is not necessary as this is a run-time parameter value to the
MM-PBSA scripts; I think we altered the radii in my_delphi.siz when using
Delphi for the solvation energy. I do not know off-hand what radii are
used for the pbsa in AMBER.

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Received on Sun Dec 23 2007 - 06:07:33 PST
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