[gmx-developers] pdb2gmx segmentation fault

[David van der Spoel]

Michel Cuendet wrote:
> 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

Since you also had problems with grompp, I sincerely doubt whether you 
compilations is OK... Do you have the possibility to test it on another 
machine with another compiler?


> 
> 
> Thanks,
> Michel
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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