rmcgibbo
commented
11 years ago This appears to be due to the same issue that you already filed in #191. A fix was committed to the latest version of msmbuilder-2.7.dev. If you'd like to pull that fix in, please update your copy of msmbuilder.
Thankes for your reply. Recently, i'm doing my protein by MSMBuilder 2.5. In my protein, there are 5567 atoms, my protein is a protein-protein compound.
When i run 'GetRandomConfs.py -c 1 -f pdb' command, it oppears the following fault:
[cuiyf@localhost hil-21-2p2]$ GetRandomConfs.py -c 1 -f pdb
MSMBuilder version 2.5.1
See file AUTHORS for a list of MSMBuilder contributors.
Copyright 2011 Stanford University. MSMBuilder comes with ABSOLUTELY NO WARRANTY. MSMBuilder is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
Please cite the following references: GR Bowman, X Huang, and VS Pande. Methods 2009. Using generalized ensemble simulations and Markov state models to identify conformational states. KA Beauchamp, GR Bowman, TJ Lane, L Maibaum, IS Haque, VS Pande. JCTC 2011. MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Timescale IS Haque, KA Beauchamp, VS Pande. In preparation. A Fast 3 x N Matrix Multiply Routine for Calculation of Protein RMSD. --------------------------------------------------------------------------------Pulling 1 for each of 99 Getting Conformations For state 0 Getting Conformations For state 1 Getting Conformations For state 2 Getting Conformations For state 3 Getting Conformations For state 4 Getting Conformations For state 5 Getting Conformations For state 6 Getting Conformations For state 7 Getting Conformations For state 8 Getting Conformations For state 9 Getting Conformations For state 10 Getting Conformations For state 11 Getting Conformations For state 12 Getting Conformations For state 13 Getting Conformations For state 14 Getting Conformations For state 15 Getting Conformations For state 16 Getting Conformations For state 17 Getting Conformations For state 18 Getting Conformations For state 19 Getting Conformations For state 20 Getting Conformations For state 21 Getting Conformations For state 22 Getting Conformations For state 23 Getting Conformations For state 24 Getting Conformations For state 25 Getting Conformations For state 26 Getting Conformations For state 27 Getting Conformations For state 28 Getting Conformations For state 29 Getting Conformations For state 30 Getting Conformations For state 31 Getting Conformations For state 32 Getting Conformations For state 33 Getting Conformations For state 34 Getting Conformations For state 35 Getting Conformations For state 36 Getting Conformations For state 37 Getting Conformations For state 38 Getting Conformations For state 39 Getting Conformations For state 40 Getting Conformations For state 41 Getting Conformations For state 42 Getting Conformations For state 43 Getting Conformations For state 44 Getting Conformations For state 45 Getting Conformations For state 46 Getting Conformations For state 47 Getting Conformations For state 48 Getting Conformations For state 49 Getting Conformations For state 50 Getting Conformations For state 51 Getting Conformations For state 52 Getting Conformations For state 53 Getting Conformations For state 54 Getting Conformations For state 55 Getting Conformations For state 56 Getting Conformations For state 57 Getting Conformations For state 58 Getting Conformations For state 59 Getting Conformations For state 60 Getting Conformations For state 61 Getting Conformations For state 62 Getting Conformations For state 63 Getting Conformations For state 64 Getting Conformations For state 65 Getting Conformations For state 66 Getting Conformations For state 67 Getting Conformations For state 68 Getting Conformations For state 69 Getting Conformations For state 70 Getting Conformations For state 71 Getting Conformations For state 72 Getting Conformations For state 73 Getting Conformations For state 74 Getting Conformations For state 75 Getting Conformations For state 76 Getting Conformations For state 77 Getting Conformations For state 78 Getting Conformations For state 79 Getting Conformations For state 80 Getting Conformations For state 81 Getting Conformations For state 82 Getting Conformations For state 83 Getting Conformations For state 84 Getting Conformations For state 85 Getting Conformations For state 86 Getting Conformations For state 87 Getting Conformations For state 88 Getting Conformations For state 89 Getting Conformations For state 90 Getting Conformations For state 91 Getting Conformations For state 92 Getting Conformations For state 93 Getting Conformations For state 94 Getting Conformations For state 95 Getting Conformations For state 96 Getting Conformations For state 97 Getting Conformations For state 98 Traceback (most recent call last): File "/usr/local/bin/GetRandomConfs.py", line 71, in
args.output, args.format)
File "/usr/local/bin/GetRandomConfs.py", line 34, in run
random_confs.SaveToPDB(output)
File "/usr/local/lib/python2.7/site-packages/msmbuilder/Trajectory.py", line 217, in SaveToPDB
PDB.WritePDBConformation(Filename,self["AtomID"], self["AtomNames"],self["ResidueNames"],self["ResidueID"],self["XYZList"][i],self["ChainID"])
File "/usr/local/lib/python2.7/site-packages/msmbuilder/PDB.py", line 2602, in WritePDBConformation
x=10*XYZ[i][0]
IndexError: index 3610 is out of bounds for axis 0 with size 3610
[cuiyf@localhost hil-21-2p2] #
My Cluster.py step is 'Cluster.py dihedral hybrid -k 100' command. Meanwhile, my trajectory is right,it is generated by Gromacs.
Then, where is my wrong ? How can i solve this problem?