[AMBER] Some Parameters In MM_PB/GBSA

From: 龚乾坤 <m201770109.hust.edu.cn>
Date: Sat, 7 Jul 2018 19:10:07 +0800 (GMT+08:00)

Dear specialist or professor,

I am a graduate student from Huazhong University of Science and Technology (HUST) in chain. Now, I am learning MM-PB/GBSA method to calculate the binding free energy, but there are some parameters which I don't understand. So I come here to ask for help.

There are two parameters in MM_PB/GBSA method I do not understand.The first is 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 ISTRNG.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? 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. Why is it happen? What are the possible reasons?

I will appreciate it if you can explain those questions, although I don't know whether I have made the questions clear.


Yours sincerely,

Qiankun Gong
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Received on Sat Jul 07 2018 - 04:30:02 PDT
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