[gmx-users] g_sas query

[Anirban Ghosh]

Hello Tsjerk & Mark,

Thanks for the reply.
Actually more important than the ions is the lipid bilayer of my system.
Actually my protein is a GPCR embedded in a lipid bilayer. So when I want to
calculate the SASA of my protein, so should I use a group
(Protein+Lipid+Ions) as the calculation group and Protein as the output
group?

Thanks again,

Anirban

On Sat, May 7, 2011 at 1:05 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 7/05/2011 4:36 PM, Anirban Ghosh wrote:
>
> Hello Tsjerk,
>
>  Thanks for the reply.
> But if I consider the ions also in the calculation group, then it is not
> wrong. Right?
>
>
> Only you know where your ions are, and whether their contribution to
> surface area means anything. Make the hybrid groups accordingly.
>
> Mark
>
>
>  Thanks,
>
>  Anirban
>
> On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:
>
>> Hey Anirban,
>>
>> I would consider the ions part of the solvent. But the procedure is right.
>>
>> Cheers,
>>
>> Tsjerk
>>
>>  On May 7, 2011 7:35 AM, "Anirban Ghosh" <reach.anirban.ghosh at gmail.com>
>> wrote:
>>
>> Hi ALL,
>>
>>  I want to calculate the SASA of a protein embedded in a bilayer along
>> with water and ions. So while using g_sas I understand that I need to supply
>> all non-solvent atoms as calculation group and Protein as the output group.
>> So I need to make a group with Protein+Lipid+Ions as the calculation group.
>> Right?
>> Thanks a lot in advance.
>>
>>  Regards,
>>
>>  Anirban
>>
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