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. 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
