[gmx-users] g_sas query

[Mark Abraham]

On 7/05/2011 7:04 PM, Anirban Ghosh wrote:
> 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?

We've answered the first part of this already.

You should read g_sas -h for clues about the groups. Only you know 
whether Protein-only output is sensible for your purpose.

Mark

> Thanks again,
>
> Anirban
>
> On Sat, May 7, 2011 at 1:05 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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 <mailto: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
>>>         <mailto: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
>>>
>>>         --
>>>         gmx-users mailing list gmx-users at gromacs.org
>>>         <mailto:gmx-users at gromacs.org>
>>>         http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>         Please search the archive at
>>>         http://www.gromacs.org/Support/Mailing_Lists/Search before
>>>         posting!
>>>         Please don't post (un)subscribe requests to the list. Use the
>>>         www interface or send it to gmx-users-request at gromacs.org
>>>         <mailto:gmx-users-request at gromacs.org>.
>>>         Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>         --
>>         gmx-users mailing list gmx-users at gromacs.org
>>         <mailto:gmx-users at gromacs.org>
>>         http://lists.gromacs.org/mailman/listinfo/gmx-users
>>         Please search the archive at
>>         http://www.gromacs.org/Support/Mailing_Lists/Search before
>>         posting!
>>         Please don't post (un)subscribe requests to the list. Use the
>>         www interface or send it to gmx-users-request at gromacs.org
>>         <mailto:gmx-users-request at gromacs.org>.
>>         Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>
>
>
>     --
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110507/4b926803/attachment.html>