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
