[AMBER] Ionic strength in MM_PBSA

From: 龚乾坤 <m201770109.hust.edu.cn>
Date: Wed, 11 Jul 2018 10:39:35 +0800 (GMT+08:00)

Dear AMBERusersanddevelopers,

In MM_PBSA, the parameter ISTRNG - Ionic strength (in mM) for the Poisson-Boltzmann solvent.

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

Ci = 146.08 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.

Thank you.

Qiankun Gong
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Received on Tue Jul 10 2018 - 20:00:03 PDT
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