[gmx-users] pdb2gmx: segmentation fault

[Kwee Hong]

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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