Re: [AMBER] neutralizing systems for AMBER TI

From: Ying-Chieh Sun <>
Date: Thu, 25 Sep 2014 11:05:01 +0800

I would say... one guideline is to keep the system neutralized as much as
possible at all lambda point simulations. ... adding ions with proper
mutation is the best way to me. HTH.

-----Original Message-----
From: Lawrenz, Morgan []
Sent: Thursday, September 25, 2014 7:02 AM
To: AMBER Mailing List
Subject: [AMBER] neutralizing systems for AMBER TI

Hi all,
For setting up a residue mutation relative free energy calc in AMBER14 with
TI/FEP, I need to neutralize my system.
The setup in leap requires a combined file with the 2 full proteins, and I
wasn't sure whether I use the real net charge on a single protein for adding
counter ions or to use the combined charge? I'd think just ions for a single
protein, despite leap complaining that the combo structure and topology file
isn't neutralized, but wanted to confirm.
Thanks a lot
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Received on Wed Sep 24 2014 - 20:30:02 PDT
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