On 01/13/11, Kwee Hong <jestan1...@yahoo.com> wrote: > > <!-- DIV {margin:0px;} --> > > > > Hi, > > > I was trying to generate topology file of my pdb using pdb2gmx. > > > Select the Force Field: > 0: GROMOS96 43a1 force > field > 1: GROMOS96 43a2 force field (improved alkane dihedrals) > 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) > 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) > 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) > 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) > 6: [DEPRECATED] > Gromacs force field (see manual) > 7: [DEPRECATED] Gromacs force field with hydrogens for NMR > 8: Encad all-atom force field, using scaled-down vacuum charges > 9: Encad all-atom force field, using full solvent charges > 4 > Opening library file /usr/share/gromacs/top/ffG53a6.rtp > Opening library file > /usr/share/gromacs/top/aminoacids.dat > Opening library file /usr/share/gromacs/top/aminoacids.dat > WARNING: masses will be determined based on residue and atom names, > this can deviate from the real mass of the atom type > Opening library file /usr/share/gromacs/top/atommass.dat > Entries in atommass.dat: 178 > WARNING: vdwradii will be determined based on residue and atom names, > this can deviate from the real mass of the atom type > Opening library file /usr/share/gromacs/top/vdwradii.dat > Entries in vdwradii.dat: 28 > Opening library file /usr/share/gromacs/top/dgsolv.dat > Entries in dgsolv.dat: 7 > Opening library file /usr/share/gromacs/top/electroneg.dat > Entries > in electroneg.dat: 71 > Opening library file /usr/share/gromacs/top/elements.dat > Entries in elements.dat: 218 > Reading complex_SurA.pdb... > Read 3163 atoms > Opening library file /usr/share/gromacs/top/xlateat.dat > 26 out of 26 lines of xlateat.dat converted succesfully > Analyzing pdb file > There are 1 chains and 0 blocks of water and 409 residues with 3163 atoms > > > chain #res #atoms > 1 'B' 409 3163 > > > All occupancy fields zero. This is probably not an X-Ray structure > Opening library file /usr/share/gromacs/top/ffG53a6.atp > Atomtype 1 > Reading residue database... (ffG53a6) > Opening library file /usr/share/gromacs/top/ffG53a6.rtp > Using default: not generating all possible dihedrals > Using default: excluding 3 bonded neighbors > Using default: generating 1,4 H--H interactions > Using default: removing impropers on same bond as a proper > Residue 108 > Sorting it all out... > Opening library file /usr/share/gromacs/top/ffG53a6.hdb > Opening library file /usr/share/gromacs/top/ffG53a6-n.tdb > Opening library file /usr/share/gromacs/top/ffG53a6-c.tdb > > > Back Off! I just backed up topol_SurA.top to ./#topol_SurA.top.1# > Processing chain 1 'B' (3163 atoms, 409 residues) > There are 629 donors and 614 acceptors > Segmentation fault > > > > Yet I encountered segmentation fault which I don't understand why this happen. > All suggestion are welcomed? > > > > > > > >
Please remember to announce your GROMACS version when discussing problems, and to try the latest one. Mark > > > > > > > >
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