Re: [AMBER] Some Parameters In MM_PB/GBSA

From: David A Case <>
Date: Sat, 7 Jul 2018 07:35:04 -0400

On Sat, Jul 07, 2018, 龚乾坤 wrote:
> ISTRNG -- Ionic strength (in mM) for the
> Poisson-Boltzmann solvent in MM_PBSA. I want to know if the protein
> is electriferous,should include protein's charge when calculating

This is a difficult question, but in practice the protein contribution is most
often ignored. Typical test tube experiments will have salt concentrations
that are many times larger than the protein cocentration, so in that case, the
distinction is unimportant. Beyond that, simulations are usually most closely
approximating the infinite dilution limit for protein.

> The second is SALTCON -- Concentration (in M) of 1-1 mobile
> counterions in solution in MM_GBSA.I don't know the meaning of SALTCON
> and how to calculate it?

SALTCON is the same as ISTRNG, except for the units used. (Historically, these
parts of Amber were written by different people).

> Next ,when I do the per-resdidue free energy
> decomposition, I find the sum of every residue binding free energy after
> decomposition don't equal to the total binding free energy in PBSA.

Some one else will have to answer this one.


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Received on Sat Jul 07 2018 - 05:00:02 PDT
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