[gmx-developers] pdb2gmx segmentation fault

Ran Friedman r.friedman at bioc.uzh.ch
Tue Jul 7 13:42:49 CEST 2009

> It seems that there are problems in pdb2gmx due to it retaining
> original residue numbers. In principle this is a good thing, and this
> was much requested. However, I suspect that your resind is actually
> larger than the number of residues (you could check this in your pdb
> file). In other words, this feature has not been implemented
> completely consistenly, I also found a problem in grompp with a new
> top file the other day, where the peptide had residue number 16, and
> the solvent had lower residue numbers. I'm not really sure how to
> continue, the code really has to be fixed.
> A workaround (if this really is the issue in your case) is to run the
> pdb files through editconf first: editconf -f in.pdb -o out.pdb as
> this program will actually renumber atoms and residue...
Only with the old editconf, and in any case it doesn't solve the problem
- I still get a segmentation fault.
Actually the solvent had residue numbers larger than those of the protein.

I forgot to mention that I get this segmentation fault with CHARMM and
OPLS, not with GROMOS or ENCAD FF. resind gives the number of water
starting from zero until the program crashes.


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