[gmx-developers] Re: pdb2gmx segmentation fault

Michel Cuendet michel.cuendet at isb-sib.ch
Tue Jun 30 11:18:01 CEST 2009

Dear David and all,

(I changed the subject back to the pdb2gmx thread)
> > Has anyone had 
> > a chance to try and reproduce the segfault with 2guo.pdb mentioned in 
> > the other thread? This one is really annoying since it requires to build 
> > topologies by hand, one chain after the other...
> I tried it with OPLS/AA or Charmm and get
> Fatal error:
> Chain identifier 'A' was used in two non-sequential blocks (residue 602, 
> atom 6295)
> Is this the error you are getting as well? It doesn't crash for me.
I'm so sorry, I forgot that I had to remove the chain name of the waters 
before applying pdb2gmx to 2GUO.pdb. The segfault appears also when 
simply stripping off all non proteic atoms :

 > grep -v HETATM 2GUO.pdb > 2GUO_nowat.pdb 
 > echo 2 | pdb2gmx -f 2GUO_nowat.pdb
[ ... normal output ... ]
There are 461 donors and 427 acceptors
There are 641 hydrogen bonds
Segmentation fault

You can also try with pdb entry 2BNR, which produces the segfault 
without modification.



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