[gmx-users] Re: pdb2gmx: segmentation fault

[Kwee Hong]

Hi all,

I've uploaded my pdb file 
at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb
Maybe someone can help me to look into it and see does it has any error.

Thanks,
Joyce



________________________________
From: Kwee Hong <jestan1985 at yahoo.com>
To: gmx-users <gmx-users at gromacs.org>
Sent: Thursday, January 13, 2011 12:21:55
Subject: pdb2gmx: segmentation fault


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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110113/bace2ab7/attachment.html>