[AMBER] How to evaluate the impact of PH on protein structures by Amber

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From: Lei Zhao <jackyzhao010.gmail.com>
Date: Thu, 24 May 2018 22:49:38 +0800

Hi everyone,
I’m wondering how to setup the system to perform MD simulation by Amber to explore the PH impact on the protein structures. In low PH condition, could we just change all Glu, Asp and His residues with their protonation states ? Would be suitable that the whole system with TIP3PBOX in neutralize condition or in the positive condition?

Anyone could give some valuable suggestions?

Thank you for your help.

Lei
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Received on Thu May 24 2018 - 08:00:02 PDT