[gmx-users] PDB2GMX PROBLEM: *** buffer overflow detected ***: pdb2gmx terminated

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 29 09:56:48 CEST 2006

Anthony Cruz wrote:
> Hi:
> I want to run a simulation of a heme protein. I found that in the gromacs site 
> the bug in the specbond.c and I download this file from bugzilla. I 
> substitute this file in the source and try to build a new rpm to install. 
> When I instal the new rpm and try to use pdb2gmx the progam stop with the 
> followin error:
> :-)  G  R  O  M  A  C  S  (-:
> *** buffer overflow detected ***: pdb2gmx terminated
> Aborted

Sounds like you have a memory problem. Try a smaller system and see...


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