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On 7/05/2011 7:04 PM, Anirban Ghosh wrote:
<blockquote
cite="mid:BANLkTik+c+sDLY_Ar=zSDTpdBG0TxsiLHg@mail.gmail.com"
type="cite">Hello Tsjerk & Mark,
<div><br>
</div>
<div>Thanks for the reply.</div>
<div>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?</div>
</blockquote>
<br>
We've answered the first part of this already.<br>
<br>
You should read g_sas -h for clues about the groups. Only you know
whether Protein-only output is sensible for your purpose.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTik+c+sDLY_Ar=zSDTpdBG0TxsiLHg@mail.gmail.com"
type="cite">
<div>Thanks again,</div>
<div><br>
</div>
<div>Anirban</div>
<div><br>
<div class="gmail_quote">On Sat, May 7, 2011 at 1:05 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff">
<div class="im"> On 7/05/2011 4:36 PM, Anirban Ghosh
wrote:
<blockquote type="cite">Hello Tsjerk,
<div><br>
</div>
<div>Thanks for the reply.</div>
<div>But if I consider the ions also in the
calculation group, then it is not wrong. Right?</div>
</blockquote>
<br>
</div>
Only you know where your ions are, and whether their
contribution to surface area means anything. Make the
hybrid groups accordingly.<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div class="h5"><br>
<br>
<blockquote type="cite">
<div>Thanks,</div>
<div><br>
</div>
<div>Anirban</div>
<div><br>
<div class="gmail_quote">On Sat, May 7, 2011 at
11:59 AM, Tsjerk Wassenaar <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:tsjerkw@gmail.com"
target="_blank">tsjerkw@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:
0pt 0pt 0pt 0.8ex; border-left: 1px solid
rgb(204, 204, 204); padding-left: 1ex;">
<p>Hey Anirban,</p>
<p>I would consider the ions part of the
solvent. But the procedure is right.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<blockquote type="cite">
<div>
<div>On May 7, 2011 7:35 AM, "Anirban
Ghosh" <<a moz-do-not-send="true"
href="mailto:reach.anirban.ghosh@gmail.com"
target="_blank">reach.anirban.ghosh@gmail.com</a>>
wrote:<br>
<br>
Hi ALL,
<div><br>
</div>
<div>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?</div>
<div>Thanks a lot in advance.</div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<font color="#888888">
<div>Anirban</div>
</font><br>
</div>
</div>
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