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

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Mon, 13 Dec 2021 17:15:13 -0500

Wow,

Thanks a lot everyone! I confess I really didn't think about just adding
Na+ then Cl-. It is so much easier than I thought! Thanks for pointing this
out.

All the best,

--
Gustavo Seabra.
On Mon, Dec 13, 2021 at 4:21 PM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> 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...
>
> Best,
>
> Matías
>
> ----- Mensaje original -----
> De: "Gustavo Seabra" <gustavo.seabra.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> 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 - 14:30:03 PST