[AMBER] neutralizing systems for AMBER TI

From: Lawrenz, Morgan <mlawrenz.amgen.com>
Date: Wed, 24 Sep 2014 23:02:09 +0000

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 - 16:30:03 PDT
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