Hi All, I'm trying to cluster a pdb trajectory format file and I'm getting odd results. The command line i'm using is:
g_cluster -f 0to7.pdb -s cysTerm.pdb -g cluster.log -o rmsd-clust.xpm -dist rmsd-dist.xvg -cl clusters.pdb -method monte-carlo -seed 4540 -niter 10000 And everything seems to go fine until the end, where it spits out the following set of results (input for fitting is C-Alpha, output C-Alpha): Reading frame 0 time -1.000 '', 2038 atoms Reading frame 1600 time 1599.000 Allocated 41086080 bytes for frames Read 1680 frames from trajectory 0to7.pdb Computing 1680x1680 RMS deviation matrix # RMSD calculations left: 0 The RMSD ranges from -nan to -nan nm Average RMSD is -nan Number of structures for matrix 1680 Energy of the matrix is -nan nm Segmentation fault I don't honestly understand whats going on here, does anybody else have any ideas? Mark Ps. I'm pretty new to using the clustering utility. -- View this message in context: http://gromacs.5086.n6.nabble.com/g-cluster-nan-segmentation-fault-error-tp5006779.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
