darn, that should have read:<br>
<br>
[ NTERM ]<br>
1<br>
[ CTERM ]<br>
288<br>
<br>
:p<br><br><div><span class="gmail_quote">On 9/14/05, <b class="gmail_sendername">Tsjerk Wassenaar</b> <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Rahul,<br>
<br>
Make an index file with two groups: <br>
<br>
[ CTERM ]<br>
1<br>
[ NTERM ]<br>
288<br>
<br>
and use that with g_mindist.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><div><span class="e" id="q_106541ce654f7a36_1"><span class="gmail_quote">On 9/14/05, <b class="gmail_sendername">Rahul Karyappa</b> <<a href="mailto:r.karyappa@ncl.res.in" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
r.karyappa@ncl.res.in</a>> wrote:</span></span></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><span class="e" id="q_106541ce654f7a36_3">
<font size="2">Dear all, <br>
I want to know the end-to-end distance of my chain
which is surrounded by ions and water molecules. I used g_mindist
command to get the values. But I am confused while selecting the
groups. The following window occurs:<br>
<br>
How many other groups do you want (>= 1) ?<br>
1<br>
Reading file topol.tpr, VERSION 3.2.1 (single precision)<br>
Reading file topol.tpr, VERSION 3.2.1 (single precision)<br>
Opening library file /usr/local/gromacs/share/top/aminoacids.dat<br>
Group 0 ( System) has 9369 elements<br>
Group 1 ( Protein) has 288 elements<br>
Group 2 ( Protein-H) has 288 elements<br>
Group 3 ( C-alpha) has 0 elements<br>
Group 4 ( Backbone) has 0 elements<br>
Group 5 ( MainChain) has 0 elements<br>
Group 6 (MainChain+Cb) has 0 elements<br>
Group 7 ( MainChain+H) has 0 elements<br>
Group 8 ( SideChain) has 288 elements<br>
Group 9 ( SideChain-H) has 288 elements<br>
Group 10 ( Prot-Masses) has 288 elements<br>
Group 11 ( Non-Protein) has 9081 elements<br>
Group 12 ( SOL) has 9081 elements<br>
Group 13 ( Other) has 9081 elements</font><br>
<br>
But how to choose the groups?<br>
Waiting for your kind reply.<br>
<br>
Rahul Karyappa<br>
NCL, Pune<br>
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gmx-users-request@gromacs.org</a>.<br><br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciencesand Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry
<br>
University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336
</blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciencesand Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4
<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336