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

[Jahn Nitschke]

Hi Mark,

Thanks for your reply. I have 8 simulations, 4 simulations of one structural variant of a ligand in solvent and 4 simulations of the same structural variants in the active center of the target protein. From each simulation I extracted the average structure of the ligand. The structural variants are macrocycles and have a common backbone, which I want to compare using confrms.
I made sure the index groups of that backbone in the index files align (same size, same atoms, same order).
Using confrms to compare pairs of averaged ligand backbones from solvent simulations works. Using confrms to compare pairs of averaged ligand backbones including one or two backbones from a complex simulation gives me the segmentation fault (core dumped) error. I hope I explained my situation clearer. Does that approach make sense to you?

Best wishes,
Jahn


On Tuesday, July 31, 2018 21:46 CEST, Mark Abraham <mark.j.abraham at gmail.com> wrote: 
 
> Hi,
> 
> On Tue, Jul 31, 2018 at 5:08 PM Jahn Nitschke <jahn.nitschke at uni-konstanz.de>
> wrote:
> 
> > 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.
> 
> Mark
> 
> 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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