<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><div>Hi all,</div><div><br></div><div>I've uploaded my pdb file at <a href="http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb">http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb</a></div><div>Maybe someone can help me to look into it and see does it has any error.</div><div><br></div><div>Thanks,</div><div>Joyce</div><meta http-equiv="content-type" content="text/html; charset=utf-8"><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><br><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Kwee Hong <jestan1985@yahoo.com><br><b><span style="font-weight: bold;">To:</span></b> gmx-users <gmx-users@gromacs.org><br><b><span
style="font-weight: bold;">Sent:</span></b> Thursday, January 13, 2011 12:21:55<br><b><span style="font-weight: bold;">Subject:</span></b> pdb2gmx: segmentation fault<br></font><br><div style="font-family:arial, helvetica, sans-serif;font-size:10pt;"><div style="font-family:arial, helvetica, sans-serif;font-size:10pt;">Hi,</div><div><div><div style="font-family:arial, helvetica, sans-serif;font-size:10pt;color:rgb(0, 0, 0);"><div style="color:rgb(0, 0, 0);font-family:arial, helvetica, sans-serif;font-size:10pt;"><br></div><div style="color:rgb(0, 0, 0);font-family:arial, helvetica, sans-serif;font-size:10pt;"> I was trying to generate topology file of my pdb using pdb2gmx.</div><div style="color:rgb(0, 0, 0);font-family:arial, helvetica, sans-serif;font-size:10pt;"><br></div><div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Select the Force Field:</i></font></div><div><font class="Apple-style-span"
face="arial, helvetica, sans-serif" size="2"><i> 0: GROMOS96 43a1 force
field </i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i> 1: GROMOS96 43a2 force field (improved alkane dihedrals)</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i> 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i> 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) </i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i> 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) </i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i> 6: [DEPRECATED]
Gromacs force field (see manual)</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i> 7: [DEPRECATED] Gromacs force field with hydrogens for NMR</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i> 8: Encad all-atom force field, using scaled-down vacuum charges</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i> 9: Encad all-atom force field, using full solvent charges </i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>4</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Opening library file /usr/share/gromacs/top/ffG53a6.rtp</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Opening library file
/usr/share/gromacs/top/aminoacids.dat</i></font></div><div><font class="Apple-style-span" face="arial,
helvetica, sans-serif" size="2"><i>Opening library file /usr/share/gromacs/top/aminoacids.dat</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>WARNING: masses will be determined based on residue and atom names,</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i> this can deviate from the real mass of the atom type</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Opening library file /usr/share/gromacs/top/atommass.dat</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Entries in atommass.dat: 178</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>WARNING: vdwradii will be determined based on residue and atom names,</i></font></div><div><font class="Apple-style-span"
face="arial, helvetica, sans-serif" size="2"><i> this can deviate from the real mass of the atom type</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Opening library file /usr/share/gromacs/top/vdwradii.dat</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Entries in vdwradii.dat: 28</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Opening library file /usr/share/gromacs/top/dgsolv.dat</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Entries in dgsolv.dat: 7</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Opening library file /usr/share/gromacs/top/electroneg.dat</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Entries
in electroneg.dat: 71</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Opening library file /usr/share/gromacs/top/elements.dat</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Entries in elements.dat: 218</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Reading complex_SurA.pdb...</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Read 3163 atoms</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Opening library file /usr/share/gromacs/top/xlateat.dat</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>26 out of 26 lines of xlateat.dat converted succesfully</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif"
size="2"><i>Analyzing pdb file</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>There are 1 chains and 0 blocks of water and 409 residues with 3163 atoms</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i><br></i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i> chain #res #atoms</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i> 1 'B' 409 3163 </i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i><br></i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>All occupancy fields zero. This is probably not an X-Ray structure</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif"
size="2"><i>Opening library file /usr/share/gromacs/top/ffG53a6.atp</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Atomtype 1</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Reading residue database... (ffG53a6)</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Opening library file /usr/share/gromacs/top/ffG53a6.rtp</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Using default: not generating all possible dihedrals</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Using default: excluding 3 bonded neighbors</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Using default: generating 1,4 H--H interactions</i></font></div><div><font
class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Using default: removing impropers on same bond as a proper</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Residue 108</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Sorting it all out...</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Opening library file /usr/share/gromacs/top/ffG53a6.hdb</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Opening library file /usr/share/gromacs/top/ffG53a6-n.tdb</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Opening library file /usr/share/gromacs/top/ffG53a6-c.tdb</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif"
size="2"><i><br></i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Back Off! I just backed up topol_SurA.top to ./#topol_SurA.top.1#</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Processing chain 1 'B' (3163 atoms, 409 residues)</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>There are 629 donors and 614 acceptors</i></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif" size="2"><i>Segmentation fault</i></font></div></div><div style="color:rgb(0, 0, 0);font-family:arial, helvetica, sans-serif;font-size:10pt;"><br></div><div style="color:rgb(0, 0, 0);font-family:arial, helvetica, sans-serif;font-size:10pt;">Yet I encountered segmentation fault which I don't understand why this happen.</div><div style="color:rgb(0, 0, 0);font-family:arial, helvetica,
sans-serif;font-size:10pt;">All suggestion are welcomed?</div><div style="color:rgb(0, 0, 0);font-family:arial, helvetica, sans-serif;font-size:10pt;"><br></div><div style="color:rgb(0, 0, 0);font-family:arial, helvetica, sans-serif;font-size:10pt;">Thanks.</div><div style="color:rgb(0, 0, 0);font-family:arial, helvetica, sans-serif;font-size:10pt;"><br></div><div style="color:rgb(0, 0, 0);font-family:arial, helvetica, sans-serif;font-size:10pt;">Joyce</div><div style="color:rgb(0, 0, 0);font-family:arial, helvetica, sans-serif;font-size:10pt;"></div>
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