[gmx-users] segmentation fault (core?==?utf-8?q? dumped) error with gmx confrms
jahn.nitschke at uni-konstanz.de
Tue Jul 31 18:07:44 CEST 2018
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. 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.
More information about the gromacs.org_gmx-users