I am testing the lastest version MSMbuilder2.5.1 on my own MD data.
I went through the tutorial completely and could repeat each step on my own computer. This should validate the installation.
But when I try to build models with my own data, I was stuck at when computing the implied Timescale.
My trajectories were converted and clustered into microstates without problem using
But when I use CalculateImpliedTimescales.py as follows,ConvertDataToHDF.py -s protein.pdb -i trj_data
Cluster.py rmsd hybrid -d 0.025
I get the following errorCalculateImpliedTimescales.py -l 1,25 -i 1 -o Data/ImpliedTimescales.dat
Anyone has a clue what the problem is?Getting 10 eigenvalues (timescales) for each lagtime...
Building MSMs at the following lag times: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]
Selected component 0 with population 0.000084
Traceback (most recent call last):
File "MSMBuilder2/bin/CalculateImpliedTimescales.py", line 87, in <module>
args.symmetrize, args.procs, args.output)
File "MSMBuilder2/bin/CalculateImpliedTimescales.py", line 48, in run
Slide=True, Symmetrize=symmetrize, nProc=nProc)
File "MSMBuilder2/lib/python2.7/site-packages/msmbuilder/MSMLib.py", line 504, in GetImpliedTimescales
lags = result.get(999999)
File "epd-7.3-64bit/lib/python2.7/multiprocessing/pool.py", line 528, in get
raise self._value
ValueError: cannot infer dimensions from zero sized index arrays
Thanks in advance.
Lizhe