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>
<div><br></div><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 href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;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></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 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 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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