[gmx-users] pdb2gmx: segmentation fault

[Mark Abraham]

On 01/13/11, Kwee Hong  <jestan1985 at yahoo.com> wrote:
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> Hi,
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>  I was trying to generate topology file of my pdb using pdb2gmx.
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> 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
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>   chain  #res #atoms
>   1 'B'   409   3163  
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> 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
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> 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
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> Yet I encountered segmentation fault which I don't understand why this happen.
> All suggestion are welcomed?
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Please remember to announce your GROMACS version when discussing problems, and to try the latest one.

Mark

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