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.abra...@anu.edu.au> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Thursday, January 13, 2011 13:43:47 Subject: Re: [gmx-users] pdb2gmx: segmentation fault On 01/13/11, Kwee Hong <jestan1...@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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