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? Thanks. Joyce
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