[gmx-users] pdb2gmx: segmentation fault

[Kwee Hong]

Hi Mark,

I tried v 4.0.7 and 4.5.1. Both experiencing the same situation.
The file is actually saved as pdb file from autodock output using pymol.

Joyce




________________________________
From: Mark Abraham <mark.abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, January 13, 2011 13:43:47
Subject: Re: [gmx-users] pdb2gmx: segmentation fault



On 01/13/11, Kwee Hong  <jestan1985 at yahoo.com> wrote:
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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