Re: [AMBER] Neutralizing a protein with unknown charge?

From: Carlos Simmerling <>
Date: Mon, 13 Dec 2021 16:12:36 -0500

yes you can do that with the addions command, just use the number 0 for
numion and it will add the right number to make it neutral.
if you aren't even sure of the sign of the charge, you can try adding both,
and it will pick the one that works:

addions solvcomplex Cl- 0
addions solvcomplex Na+ 0

On Mon, Dec 13, 2021 at 3:56 PM Gustavo Seabra <>

> Hi all,,
> This may be a weird question but...
> Is there a way in LEaP to automagically add the correct amount of Na+/Cl-
> ions to neutralize any system, without the need for us to know a priori if
> the system is positively or negatively charged (or even neutral)?
> The reason: I want to prepare a LEaP input file that can work with a large
> number of proteins in a database. Some of them may be positively charged,
> some may be negatively charged or some may even be neutral. I'd like to be
> able to automate the process of creating the parameters using LEaP to work
> with all of them, irrespective of the charge.
> Any suggestions are highly appreciated!
> Thanks a lot!
> --
> Gustavo Seabra.
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Received on Mon Dec 13 2021 - 13:30:02 PST
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