[gmx-developers] Re: pdb2gmx segmentation fault

[David van der Spoel]

Michel Cuendet wrote:
> 
> 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
> 
I am now doing this using the latest git source, but it works fine on my 
Mac.
However, with a slightly older develop code it fails. With the .4.0.x 
release tit works fine though.
It seems to be a temporary bug that was resolved again.

Plz upgrade...

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