<br /><br /><span>On 01/13/11, <b class="name">Kwee Hong </b> <jestan1985@yahoo.com> wrote:</span><blockquote cite="mid:385614.48828.qm@web31407.mail.mud.yahoo.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span><p><style type="text/css"><!-- DIV {margin:0px;} --></style><table><tbody><tr><td><p></p><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></div></div></div></td></tr></tbody></table></p></span></div></blockquote><br />Please remember to announce your GROMACS version when discussing problems, and to try the latest one.<br /><br />Mark<br /><blockquote cite="mid:385614.48828.qm@web31407.mail.mud.yahoo.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span><p><table><tbody><tr><td><br /></td></tr></tbody></table></p></span></div></blockquote>