Respected amber users
we are trying to analyse the amber trajecteries that we got after
performing simulated annealing. I am performing these experiments for first
time and do not have much knowledge of it.
I intend to use cpptraj to formulate low energy clusters of trajectrories
with rmsd values calculated from their respective centroid. However, I am
getting the following error:
ACTION OUTPUT:
ANALYSIS: Performing 1 analyses:
0: [cluster C0 dbscan minpoints 25 epsilon 0.9 sievetoframe rms :1-10
sieve 10 out cnumvtime.dat 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 [:1-10] corresponds to 103 atoms.
Estimated pair-wise matrix memory usage: > 0.244 kB
Pair-wise matrix set up with sieve, 100 frames, 10 sieved frames.
Calculating pair-wise distances.
0% 11% 22% 33% 44% 56% 67% 78% 89% Complete.
Memory used by pair-wise matrix and other cluster data: 0.732 kB
0% 11% 22% 33% 44% 56% 67% 78% 89% 100% Complete.
No clusters found.
Cluster timing data:
TIME: Cluster Init. : 0.0000 s ( 0.34%)
TIME: Pairwise Calc.: 0.0002 s ( 66.78%)
TIME: Clustering : 0.0000 s ( 7.80%)
TIME: Cluster Post. : 0.0000 s ( 0.68%)
TIME: Cluster renumbering/sieve restore 0.0000 s ( 0.00%)
TIME: Find best rep. 0.0000 s ( 0.00%)
TIME: Info calc 0.0000 s ( 0.00%)
TIME: Summary calc 0.0000 s ( 0.00%)
TIME: Coordinate writes 0.0000 s ( 0.00%)
TIME: Total: 0.0003 s
TIME: Analyses took 0.0004 seconds.
DATASETS (3 total):
_DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100 (123.624 kB) 103
atoms
C0 "C0" (integer), size is 0
C0[PWD] "C0[PWD]" (cluster matrix), size is 45
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.
RUN TIMING:
TIME: Init : 0.0001 s ( 0.35%)
TIME: Trajectory Process : 0.0270 s ( 97.35%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0004 s ( 1.27%)
TIME: Data File Write : 0.0000 s ( 0.15%)
TIME: Other : 0.0002 s ( 0.01%)
TIME: Run Total 0.0277 s
---------- RUN END ---------------------------------------------------
details of the input command and log file has been attached. It would be
very helpful if someone can guide me through.
Thank you
with regards
--
*With regards*
*Rajbinder Kaur Virk*
*Research Scholar *
*Department of Biophysics*
*Panjab University *
*Chandigarh-160014*
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Received on Mon Nov 19 2018 - 05:00:02 PST
