[AMBER] How to proceed if system charge is non-zero and non-integral

From: Amit Sharma (Asstt. Prof., MCARS) <"Amit>
Date: Thu, 10 Dec 2020 18:07:14 +0530


Protein (solvated) that I am planning to simulate contains a chromophore in
it. Total charge on the system in this case is -5.844897 hence,
non-integral and non-zero. If I neutralize the charge by adding Na+ ions,
it adds six Na+ and my system now shows a charge of 0.155103, which again
is non-zero and non-integral.

Can someone plz suggest how I can reduce the total charge on the system to
zero? Else, is it fine to go ahead with simulation with non-integral charge
of ~0.15?



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Received on Thu Dec 10 2020 - 05:00:02 PST
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