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

From: Debarati DasGupta <>
Date: Mon, 13 Dec 2021 21:19:15 +0000

Hi Gustavo
In my file I usually have addions pro Na+ 0 as well as addions pro Cl- 0
This is helpful as irrespective of the charge on the protein, my leap script adds Na+ or Chloride and neutralizes it .

Hope I could help!

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From: Gustavo Seabra<>
Sent: Monday, December 13, 2021 3:56 PM
To: AMBER Mailing List<>
Subject: [AMBER] Neutralizing a protein with unknown charge?

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 - 13:30:03 PST
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