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On 21/07/2011 11:38 PM, Anna Marabotti wrote:
<blockquote cite="mid:5D13115144F3496197A113237A7DAE20@AnnaNetbook"
type="cite">
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<div><font face="Arial" size="2"><span class="875441513-21072011">Hi
folks</span></font></div>
<div><font face="Arial" size="2"><span class="875441513-21072011">here
I am with another kind of error, this time analysing my
trajectory of the rhombic dodecahedron dimeric system with
g_cluster.</span></font></div>
<div><font face="Arial" size="2"><span class="875441513-21072011">I
used the following command:</span></font></div>
<div><font face="Arial" size="2"><span class="875441513-21072011">g_cluster
-f prot_boxdodfull_mol.xtc s prot_boxdodfull_molren.tpr -o
prot_boxdodfull_clust.xpm -sz prot_boxdodfull_clustsize.xvg
-tr prot_boxdodfull_clusttrans.xpm -ntr
prot_boxdodfull_clusttrans.xvg -clid
prot_boxdodfull_clustovertime.xvg -cl
prot_boxdodfull_clusters.pdb -av -cutoff 0.25 -method gromos
-b 10000</span></font></div>
</blockquote>
<br>
I'd suggest starting with a small trajectory and a basic clustering
method to help you eliminate possible sources of problems. If things
are working, add complexity.<br>
<br>
<blockquote cite="mid:5D13115144F3496197A113237A7DAE20@AnnaNetbook"
type="cite">
<div><font face="Arial" size="2"><span class="875441513-21072011"></span></font> </div>
<div><font face="Arial" size="2"><span class="875441513-21072011">(the
command is inspired to that shown in Tsjerk's tutorial, with
some changes, and with the missing -g flag - I forgot to add
it). For both least square fit+RMSD calculation and output I
used option 2 (Protein-H).</span></font></div>
<div><font face="Arial" size="2"><span class="875441513-21072011"></span></font> </div>
<div><font face="Arial" size="2"><span class="875441513-21072011">The
.tpr file is derived from the renumbered .gro file in which
I can see both subunits of my protein (as suggested
sometimes ago by Justin), created with the command: grompp
-f full.mdp -c prot_boxdodfull_molren.gro -o
prot_boxdodfull_molren.tpr -p topol.top, in which full.mdp
is the file I used for the full MD.</span></font></div>
</blockquote>
<br>
I don't think you need a new .tpr, or a .tpr at all. Nothing about
the clustering method requires knowledge of molecule or parameter
definitions, so the original .tpr or the coordinate file that made
it will do. Surely the clustering is based on RMS after fitting of
the two structures under consideration, and now even the coordinates
in the g_cluster -s file don't matter. Pre-processing the trajectory
can matter - you probably want whole molecules in the simulation
cell.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:5D13115144F3496197A113237A7DAE20@AnnaNetbook"
type="cite">
<div><font face="Arial" size="2"><span class="875441513-21072011"></span></font> </div>
<div><font face="Arial" size="2"><span class="875441513-21072011">With
this command, I obtained the following output, that I'm
copying and pasting here (I cut some parts because of the
length of the message, but I think they are not necessary):</span></font></div>
<div><span class="875441513-21072011"><span lang="IT">
<p><font face="Arial" size="2">Reading frame 0 time
10000.000 </font></p>
<p><font face="Arial" size="2">Reading frame 1 time
10005.000 </font></p>
<p><font face="Arial" size="2">Reading frame 2 time
10010.000 </font></p>
<p><font face="Arial" size="2">Reading frame 3 time
10015.000 </font></p>
<p><font face="Arial" size="2">Reading frame 4 time
10020.000 </font></p>
<p><font face="Arial" size="2">Reading frame 5 time
10025.000 </font></p>
<p><font face="Arial" size="2">Reading frame 6 time
10030.000 </font></p>
<p><span class="875441513-21072011"><font face="Arial"
size="2">............................................</font></span></p>
<span class="875441513-21072011"><span lang="IT">
<p>Reading frame 3000 time 25000.000 </p>
<p>Reading frame 4000 time 30000.000 </p>
<p>Last frame 4000 time 30000.000 </p>
<p>Allocated 280347120 bytes for frames</p>
<p>Read 4001 frames from trajectory <span
class="875441513-21072011">prot</span>_boxdodfull_mol.xtc</p>
<p>Computing 4001x4001 RMS deviation matrix</p>
<p># RMSD calculations left: 7998000 </p>
<p># RMSD calculations left: 7994001 </p>
<p># RMSD calculations left: 7990003 </p>
<p># RMSD calculations left: 7986006 </p>
<p><span class="875441513-21072011">.......................................................................................</span></p>
<span class="875441513-21072011">
<p style="MARGIN: 0cm 0cm 0pt" class="MsoPlainText"><font
face="Courier New" size="2">The RMSD ranges from
0.0776069 to 0.282556 nm<br>
Average RMSD is 0.18743<br>
Number of structures for matrix 4001<br>
Energy of the matrix is 281.481 nm<br>
WARNING: rmsd minimum 0 is below lowest rmsd value
0.0776069<br>
Making list of neighbors within cutoff<span
style="mso-spacerun: yes"> </span></font></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoPlainText"><span
style="mso-spacerun: yes"></span><font
face="Courier New" size="2">Finding clusters<span
style="mso-spacerun: yes"> </span>1<br>
<br>
Found 1 clusters<br>
<br>
Writing average structure for each cluster to <span
class="875441513-21072011">prot</span>_boxdodfull_clusters.pdb<br>
Counted 0 transitions in total, max 0 between two
specific clusters<br>
<br>
-------------------------------------------------------<br>
Program g_cluster, VERSION 4.5.3<br>
Source code file: matio.c, line: 953<br>
<br>
Fatal error:<br>
hi (0.000000) <= lo (0.000000)<br>
For more information and tips for troubleshooting,
please check the GROMACS<br>
website at
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------</font><br>
</p>
</span></span></span></span></span></div>
<div><font face="Arial" size="2"><span class="875441513-21072011">I
tried to look at the documentation, but found only 1 similar
problem, using the g_rmsdist command, but there is not a
solution to the problem. I see the warning message claiming
that the rmsd minimum 0 is below lowest rmsd value, but I
don't know how to manage it. Could the .tpr file I used be
the cause of the problem?</span></font></div>
<div><font face="Arial" size="2"><span class="875441513-21072011">Could
anybody help me please?</span></font></div>
<div><font face="Arial" size="2"><span class="875441513-21072011">Thank
you so much for your continue support</span></font></div>
<div><font face="Arial" size="2"><span class="875441513-21072011">Anna</span></font></div>
<div> </div>
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<div dir="ltr" align="left"><font face="Arial" size="2">__________________________________________________________________</font></div>
<div align="left"><font face="Arial" size="2">Anna Marabotti,
Ph.D.</font></div>
<div align="left"><font face="Arial" size="2">Laboratory of
Bioinformatics and Computational Biology</font></div>
<div align="left"><font face="Arial" size="2">Institute of Food
Science - CNR</font></div>
<div align="left"><font face="Arial" size="2">Via Roma, 64</font></div>
<div align="left"><font face="Arial" size="2">83100 Avellino</font></div>
<div align="left"><font face="Arial" size="2">Phone: +39 0825
299651</font></div>
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781585</font></div>
<div align="left"><font face="Arial" size="2">E-mail: <a
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title="mailto:amarabotti@isa.cnr.it"
href="mailto:amarabotti@isa.cnr.it">amarabotti@isa.cnr.it</a></font></div>
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annam1972</font></div>
<div align="left"><font face="Arial" size="2">Web site: <a
moz-do-not-send="true"
title="http://bioinformatica.isa.cnr.it/anna/anna.htm"
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</a></font></div>
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