[AMBER] Adding ions to implicit solvent models

From: Conrad F Li <conradliste.utexas.edu>
Date: Wed, 29 Jul 2020 20:17:34 -0500


I am new to using Amber. After running saveAmberParams in the tleap, I
received the warning

Warning: The unperturbed charge of the unit (-4.000000) is not zero.

I have seen Amber tutorials using explicit water models which resolved this
warning by adding Na+ and Cl- ions (i.e. addIons mol Na+ 0 and addIons mol
Cl- 0) until the charge was neutralized. However, if I am using an implicit
solvent model (i.e. igb=8), do I still need to neutralize the charge by
adding ions? On a more general note, how would I go about adding ions in
tleap (even if it was not for the sake neutralizing the molecule) for
implicit solvent simulations?

Thank you,
Conrad Li
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Received on Wed Jul 29 2020 - 18:30:02 PDT
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