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<DIV><FONT size=2 face=Arial><SPAN class=875441513-21072011>Hi
folks</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><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 size=2 face=Arial><SPAN class=875441513-21072011>I used the following
command:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><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>
<DIV><FONT size=2 face=Arial><SPAN
class=875441513-21072011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><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 size=2 face=Arial><SPAN
class=875441513-21072011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><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>
<DIV><FONT size=2 face=Arial><SPAN
class=875441513-21072011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><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 size=2 face=Arial>Reading frame 0 time 10000.000 </FONT></P>
<P><FONT size=2 face=Arial>Reading frame 1 time 10005.000 </FONT></P>
<P><FONT size=2 face=Arial>Reading frame 2 time 10010.000 </FONT></P>
<P><FONT size=2 face=Arial>Reading frame 3 time 10015.000 </FONT></P>
<P><FONT size=2 face=Arial>Reading frame 4 time 10020.000 </FONT></P>
<P><FONT size=2 face=Arial>Reading frame 5 time 10025.000 </FONT></P>
<P><FONT size=2 face=Arial>Reading frame 6 time 10030.000 </FONT></P>
<P><SPAN class=875441513-21072011><FONT size=2
face=Arial>............................................</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 size=2
face="Courier New">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 size=2 face="Courier New">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
http://www.gromacs.org/Documentation/Errors<BR>-------------------------------------------------------</FONT><BR></P></SPAN></SPAN></SPAN></SPAN></SPAN></DIV>
<DIV><FONT size=2 face=Arial><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 size=2 face=Arial><SPAN class=875441513-21072011>Could anybody help
me please?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=875441513-21072011>Thank you so much
for your continue support</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=875441513-21072011>Anna</SPAN></FONT></DIV>
<DIV> </DIV>
<DIV align=left>
<DIV dir=ltr align=left><FONT size=2
face=Arial>__________________________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Laboratory of Bioinformatics and
Computational Biology</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Institute of Food Science -
CNR</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Via Roma, 64</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>83100 Avellino</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Phone: +39 0825 299651</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Fax: +39 0825 781585</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>E-mail: <A
title=mailto:amarabotti@isa.cnr.it
href="mailto:amarabotti@isa.cnr.it">amarabotti@isa.cnr.it</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Skype account: annam1972</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web site: <A
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>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"When a man with a gun meets a man with
a pen, the man with the gun is a dead man"</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>(Roberto Benigni, about Roberto
Saviano)</FONT></DIV></DIV>
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