Hello,
I'm absolutely new to cluster analysis, so I'm getting problems following
the tutorial
http://www.amber.utah.edu/AMBER-workshop/London-2015/Cluster/
. Here is my cpptraj input:
parm rat.parm7
trajin rat_ph5.nc
strip :WAT,Cl- outprefix pep
cluster C0 dbscan minpoints 25 epsilon 0.9 sievetoframe rms sieve 10 random
out cnumvtime.dat sil Sil summary summary.dat info info.dat cpopvtime
cpopvtime.agr normframe repout rep repfmt pdb singlerepout singlerep.nc
singlerepfmt netcdf avgout Avg avgfmt restart
run
And this is what I get after the "classic" trajectory processing:
ACTION OUTPUT:
ANALYSIS: Performing 1 analyses:
0: [cluster C0 dbscan minpoints 25 epsilon 0.9 sievetoframe rms sieve 10
random out cnumvtime.dat sil Sil summary summary.dat info info.dat
cpopvtime cpopvtime.agr normframe repout rep repfmt pdb singlerepout
singlerep.nc singlerepfmt netcdf avgout Avg avgfmt restart]
Starting clustering.
Mask [*] corresponds to 354 atoms.
Calculating pair-wise distances.
Random_Number: seed is <= 0, using wallclock time as seed (11931638)
Estimated pair-wise matrix memory usage: > 36.594 MB
Pair-wise matrix set up with sieve, 42771 frames, 4278 sieved frames.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete.
Memory used by pair-wise matrix and other cluster data: 36.808 MB
Starting DBSCAN Clustering:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
No clusters found.
Cluster timing data:
TIME: Cluster Init. : 0.0000 s ( 0.00%)
TIME: Pairwise Calc.: 44.4838 s ( 99.73%)
TIME: Clustering : 0.1219 s ( 0.27%)
TIME: Cluster Post. : 0.0000 s ( 0.00%)
TIME: Total: 44.6057 s
TIME: Analyses took 44.6058 seconds.
DATASETS (2 total):
_DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 42771 (182.718 MB)
Box Coords, 354 atoms
C0 "C0" (integer), size is 0
DATAFILES (2 total):
cnumvtime.dat (Standard Data File): C0
cpopvtime.agr (Grace File):
Warning: Set 'C0' contains no data.
Warning: File 'cnumvtime.dat' has no sets containing data.
Warning: File 'cpopvtime.agr' has no sets containing data.
So, I guess the problem is in this C0, and I bet it's a trivial one, but I
have no clues. Can you help me?
Thanks!
Elisa
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Received on Wed Jun 28 2017 - 09:00:02 PDT
