[gmx-developers] pdb2gmx segmentation fault

[Michel Cuendet]

Dear all,

The last CVS version of pdb2gmx seems to be broken. I haven't tried to 
download the current GIT version yet, please tell me if there have been 
any updates.

For some pdb files (not all), it produces a Seg Fault. For some others, 
it seems not to find normal atoms in the rtp file. One example to 
reproduce the problem is 2GUO.pdb, with the first asymetrical unit, i.e. 
chain A,B,C.

echo 2 | ~/Gromacs/gromacs-4.0.cvs_12.6.2009/i686_gcc4.2.4/bin/pdb2gmx 
-f 2GUO_ABC.pdb

[... usual output ...]
Reading 2GUO_ABC.pdb...
WARNING: all CONECT records are ignored
Read 'HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2; 3 ALPHA CHAIN; 6 
HEAVY CHAIN (RESIDUES 25-299); BETA-2-MICROGLOBULIN; PEPTIDE; 18 
LB39-AA', 3442 atoms
Opening library file 
/export/home/mcuendet/Gromacs/gromacs-4.0.cvs_12.6.2009/i686_gcc4.2.4/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 3 chains and 1 blocks of water and 555 residues with 3442 atoms

  chain  #res #atoms
  1 'A'   275   2251
  2 'B'   100    837
  3 'C'     9     57
  4 '-'   297    297  (only water)

WARNING: there were 0 atoms with zero occupancy and 8 atoms with
         occupancy unequal to one (out of 3442 atoms). Check your pdb file.
Opening library file 
/export/home/mcuendet/Gromacs/gromacs-4.0.cvs_12.6.2009/i686_gcc4.2.4/share/gromacs/top/ffG45a3.atp
Atomtype 1
Reading residue database... (ffG45a3)
Opening library file 
/export/home/mcuendet/Gromacs/gromacs-4.0.cvs_12.6.2009/i686_gcc4.2.4/share/gromacs/top/ffG45a3.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 96
Sorting it all out...
Opening library file 
/export/home/mcuendet/Gromacs/gromacs-4.0.cvs_12.6.2009/i686_gcc4.2.4/share/gromacs/top/ffG45a3.hdb
Opening library file 
/export/home/mcuendet/Gromacs/gromacs-4.0.cvs_12.6.2009/i686_gcc4.2.4/share/gromacs/top/ffG45a3-n.tdb
Opening library file 
/export/home/mcuendet/Gromacs/gromacs-4.0.cvs_12.6.2009/i686_gcc4.2.4/share/gromacs/top/ffG45a3-c.tdb

Back Off! I just backed up topol.top to ./#topol.top.6#
Processing chain 1 'A' (2251 atoms, 275 residues)
There are 461 donors and 427 acceptors
There are 641 hydrogen bonds

Program received signal SIGSEGV, Segmentation fault.
0xb7e5b727 in set_histp ()
   from 
/export/home/mcuendet/Gromacs/gromacs-4.0.cvs_12.6.2009//i686_gcc4.2.4//lib/libgmxpreprocess.so.0
Current language:  auto; currently asm


Thanks,
Michel