[gmx-users] segmentation fault (core?==?utf-8?q? dumped) error with gmx confrms

Mark Abraham mark.j.abraham at gmail.com
Tue Jul 31 19:46:21 CEST 2018


On Tue, Jul 31, 2018 at 5:08 PM Jahn Nitschke <jahn.nitschke at uni-konstanz.de>

> Dear community,
> i have a segmentation fault (core dumped) error with gmx confrms.
> In more detail: i extracted the average structure of four different
> ligands with the same backbone from a solvent simulation and wanted to use
> confrms to calculate the rmsd between the backbone. This works.
> I also extracted the average structure of the same ligands from a
> simulation in its target molecule, a protein. When I use confrms to compare
> the backbone structure to the solvent structure I get the segmentation
> fault error.

How are you comparing "backbone structure" to "solvent structure?" I assume
the crash relates from poor checking of whether the index groups have the
right sizes and range to work, but part of the problem might be trying to
do something that doesn't make sense. If it does make sense, then we would
appreciate opening an issue at https://redmine.gromacs.org and attaching
enough files for us to replicate the issue.


Comparing backbones from the complex simulation to backbones from the
> complex simulation also gives the error. So I assume, it must be something
> with the average structures obtained from the complex simulation.
> I made sure, the atoms of the ligand are sorted exactly the same in the
> index files, i tried not using the fit option or the name option and also
> two gromacs versions:  2016.4 and version 5.2.1. Am I missing something
> obvious?
> Any help is appreciated.
> Best wishes,
> Jahn Nitschke
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