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

From: Matias Machado <>
Date: Mon, 13 Dec 2021 18:20:10 -0300 (UYT)

Dear Gustavo,

Something like this should work:

# Load molecule
  protein = loadpdb xxx.pdb
  charge protein

# Add solvate and counterions.
  solvateOct protein TIP3PBOX 12.0
  addIonsRand protein NA 0
  addIonsRand protein CL 0

  charge protein

If your protein is positive charged then leap will pint the following message and no NA ions is added

     unit charge = 11; ion1 charge = 1;
     can't neutralize.

The correct amount of CL ions is added (in this case 11)

The same happens for a negative charged protein...

Note, this just neutralize the system, no salt is added...



----- Mensaje original -----
De: "Gustavo Seabra" <>
Para: "AMBER Mailing List" <>
Enviados: Lunes, 13 de Diciembre 2021 17:55:47
Asunto: [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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