<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 7/05/2011 4:36 PM, Anirban Ghosh wrote:
<blockquote
cite="mid:BANLkTimPxtfvBSJaznrWUza+PxwbHKKmHw@mail.gmail.com"
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>
Only you know where your ions are, and whether their contribution to
surface area means anything. Make the hybrid groups accordingly.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTimPxtfvBSJaznrWUza+PxwbHKKmHw@mail.gmail.com"
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">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 class="h5">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>
--<br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use
the<br>
www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
<br>
--<br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use
the<br>
www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
<br>
</body>
</html>