Hi folks here I am with another kind of error, this time analysing my trajectory of the rhombic dodecahedron dimeric system with g_cluster. I used the following command: g_cluster -f prot_boxdodfull_mol.xtc s prot_boxdodfull_molren.tpr -o prot_boxdodfull_clust.xpm -sz prot_boxdodfull_clustsize.xvg -tr prot_boxdodfull_clusttrans.xpm -ntr prot_boxdodfull_clusttrans.xvg -clid prot_boxdodfull_clustovertime.xvg -cl prot_boxdodfull_clusters.pdb -av -cutoff 0.25 -method gromos -b 10000 (the command is inspired to that shown in Tsjerk's tutorial, with some changes, and with the missing -g flag - I forgot to add it). For both least square fit+RMSD calculation and output I used option 2 (Protein-H). The .tpr file is derived from the renumbered .gro file in which I can see both subunits of my protein (as suggested sometimes ago by Justin), created with the command: grompp -f full.mdp -c prot_boxdodfull_molren.gro -o prot_boxdodfull_molren.tpr -p topol.top, in which full.mdp is the file I used for the full MD. With this command, I obtained the following output, that I'm copying and pasting here (I cut some parts because of the length of the message, but I think they are not necessary): Reading frame 0 time 10000.000
Reading frame 1 time 10005.000 Reading frame 2 time 10010.000 Reading frame 3 time 10015.000 Reading frame 4 time 10020.000 Reading frame 5 time 10025.000 Reading frame 6 time 10030.000 ............................................ Reading frame 3000 time 25000.000 Reading frame 4000 time 30000.000 Last frame 4000 time 30000.000 Allocated 280347120 bytes for frames Read 4001 frames from trajectory prot_boxdodfull_mol.xtc Computing 4001x4001 RMS deviation matrix # RMSD calculations left: 7998000 # RMSD calculations left: 7994001 # RMSD calculations left: 7990003 # RMSD calculations left: 7986006 ............................................................................ ........... The RMSD ranges from 0.0776069 to 0.282556 nm Average RMSD is 0.18743 Number of structures for matrix 4001 Energy of the matrix is 281.481 nm WARNING: rmsd minimum 0 is below lowest rmsd value 0.0776069 Making list of neighbors within cutoff Finding clusters 1 Found 1 clusters Writing average structure for each cluster to prot_boxdodfull_clusters.pdb Counted 0 transitions in total, max 0 between two specific clusters ------------------------------------------------------- Program g_cluster, VERSION 4.5.3 Source code file: matio.c, line: 953 Fatal error: hi (0.000000) <= lo (0.000000) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I tried to look at the documentation, but found only 1 similar problem, using the g_rmsdist command, but there is not a solution to the problem. I see the warning message claiming that the rmsd minimum 0 is below lowest rmsd value, but I don't know how to manage it. Could the .tpr file I used be the cause of the problem? Could anybody help me please? Thank you so much for your continue support Anna __________________________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm "When a man with a gun meets a man with a pen, the man with the gun is a dead man" (Roberto Benigni, about Roberto Saviano)
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