Re: [AMBER] Adding ions to implicit solvent models

From: Bill Ross <>
Date: Thu, 30 Jul 2020 02:00:18 -0700

In leap, > help addonsAlso you've likely skimmed the examples of it in the tutorials?The question of your case has likely been answered before and worst case is covered in the manual, but isn't in my experience. Bill RossAI:
-------- Original message --------From: Conrad F Li <> Date: 7/29/20 6:17 PM (GMT-08:00) To: Subject: [AMBER] Adding ions to implicit solvent models Hello,I am new to using Amber. After running saveAmberParams in the tleap, Ireceived the warningWarning: The unperturbed charge of the unit (-4.000000) is not zero.I have seen Amber tutorials using explicit water models which resolved thiswarning by adding Na+ and Cl- ions (i.e. addIons mol Na+ 0 and addIons molCl- 0) until the charge was neutralized. However, if I am using an implicitsolvent model (i.e. igb=8), do I still need to neutralize the charge byadding ions? On a more general note, how would I go about adding ions intleap (even if it was not for the sake neutralizing the molecule) forimplicit solvent simulations?Thank you,Conrad Li_______________________________________________AMBER mailing listAMBER.ambermd.org
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Received on Thu Jul 30 2020 - 02:30:02 PDT
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