Re: AMBER: Addions in GB Mode?

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Mon, 20 Oct 2008 06:12:52 -0400

it is not necessary, and can be very problematic. you can set overall
ionic strength if desired.
keep in mind that this is approximate.



On Mon, Oct 20, 2008 at 5:25 AM, parul sharma <sharmaparul7373.gmail.com> wrote:
> 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.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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Received on Mon Oct 20 2008 - 05:09:49 PDT
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