Re: [AMBER] Ionic strength in MM_PBSA

From: David A Case <>
Date: Wed, 11 Jul 2018 09:40:24 -0400

On Wed, Jul 11, 2018, 龚乾坤 wrote:
> In my protein system, there are two peptide chains, each of them has six
> positive charge.
> The system also includes 4231 water molecules and periodic boundary
> condition. So I add 12 Cl- to neutralize this system and the volume
> is 136449.9 A^3. The following is my calculation process about Ionic
> strength:
> The ionic strength I = 0.5×Ci×(-1)^2 = 73.04 mM/L
> Here I ignore the protein's charge, the Ci is the concentration of
> Cl-. I want to know whether the calculation is ture. If my calculation
> is wrong, and how to calculate the Ionic strength in my system.

If you only have neutralizing counterions (just enough to lead to a net
charge of zero), those ions are partially "tied up" in neutralizing the
peptide positive charge, and cannot contribute as effectively as they
might to screening charge-charge interactions.

I've never really seen a discussion of this point, but my feeling is
that your simulation is closer to an ionic strength of zero than to 73
mM. You might see if your MM-PBSA numbers depend much on what
ionic strength you use. You might also want to match the ionic strength
of the relevant experiment, rather than that of the explicit solvent


1. "M" means moles/liter, so you don't want the "/L" in your

2. The factor of 0.5 in you equation assumes a 1-1 salt, which you don't
have (you have no Na+ ions). So there is no correct way to compute the
ionic strength of your simulation. If you wish to mimic a non-zero
ionic environment, you would need to add more Na+ and Cl- ions.


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Received on Wed Jul 11 2018 - 07:00:02 PDT
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