AMBER Archive (2008)

Subject: Re: AMBER: Addions in GB Mode?

From: parul sharma (sharmaparul7373_at_gmail.com)
Date: Mon Oct 20 2008 - 04:25:22 CDT

Dear Amber Users,

I am also doing my calculations using GB-OBC approximation, but i haven't
included the counter ions in my peptide. I remember i read somewhere that if
we using GB approach it's not necessary to add counter ions in peptides, but
i am still not sure so if somebody please could help us out with this query
we will be really thankful.

Thanks
Parul Sharma
Phd fellow
Durban University of Technology
South Africa

On Sun, Oct 19, 2008 at 7:04 PM, Rogelio Hernández <rahl_emc_at_yahoo.com.mx>wrote:

> Dear Amber Users
>
> Probably this is a very easy question, I apologize for that. I want to know
> if is correct to add counterions to my system to neutralize the charges of
> my protein if I want to use GB mode.
>
> Thanks in advance
>
> Rogelio Hernandez
>
> __________________________________________________
> Correo Yahoo!
> Espacio para todos tus mensajes, antivirus y antispam ¡gratis!
> Regístrate ya - http://correo.yahoo.com.mx/
>

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