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.abra...@anu.edu.au
<mailto:mark.abra...@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
<tsje...@gmail.com <mailto:tsje...@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.gh...@gmail.com
<mailto:reach.anirban.gh...@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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