On Wed, Sep 12, 2012 at 8:08 AM, Jonathan Gough
<jonathan.d.gough.gmail.com>wrote:
> Thanks David,
>
> I will check that.
>
> I was using AmberTools 12, Amber 12 and leaprc.ff12SB
>
> It was curious to me that when I did use the formalism
> addions *unit* Na+ 0
>
> that i got the error message Can't neutralize.
>
I think you saw Dave's suggestion for fixing this, but I may not be
understanding your response here. Just to clarify, you need to select ion
parameters for the solvent model you are using. For instance, if you use
TIP3P, you need to have the command
loadamberparams frcmod.ionsjc_tip3p
in order to load the appropriate ion parameters for TIP3P. This should be
described in the AmberTools manual.
> on a related note, is it necessary or good/bad form to charge balance a
> protein for a minimization and/or basic MD run in explicit or implicit
> solvent?
>
Explicit solvent, I would advise neutralizing your unit cell. (More than
that, I would suggest using "addIonsRand" in tleap to add ions randomly
throughout your solvent box rather than in pockets of largest, favorable
electrostatic potential).
Implicit solvent, do NOT use explicit ions (unit neutralization is
unnecessary). Implicit solvent models treat ions implicitly (e.g., GB uses
a debye screening parameter, and the Boltzmann part of the
Poisson-Boltzmann equation is the part that accounts for ionic strength
effects).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 12 2012 - 06:00:05 PDT
