Dear amber users,
I’ve been trying to run a cluster analysis over multiple trajectory files, each one being a portion of the same run. I’ve encountered the following error message:
AMBERHOME/bin/cpptraj -i nat2-0_cluster.in
CPPTRAJ: Trajectory Analysis. V16.16
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 11/03/16 16:42:16
| Available memory: 1.417 GB
INPUT: Reading input from 'nat2-0_cluster.in'
[parm native2.parm]
Reading 'native2.parm' as Amber Topology
[loadcrd nat2_md-qm.nc name nat2-0]
Reading 'nat2_md-qm.nc' as Amber NetCDF
Warning: COORDS data sets do not store times.
Loading trajectory 'nat2_md-qm.nc' as 'nat2-0'
.
.
.
[loadcrd nat-ew2-0_mdqm19.nc name nat2-0]
Reading 'nat-ew2-0_mdqm19.nc' as Amber NetCDF
Appending trajectory 'nat-ew2-0_mdqm19.nc' to COORDS data set 'nat2-0'
----- nat-ew2-0_mdqm19.nc (1-250, 1) -----
[reference nat2_md-qm_0.pdb [ref]]
Reading 'nat2_md-qm_0.pdb' as PDB
Read CRYST1 info from PDB: a=62.134 b=62.134 c=62.134 alpha=109.47 beta=109.47 gamma=109.47
Warning: Low precision truncated octahedron angles detected (109.47 vs 109.471).
Warning: If desired, the 'box' command can be used during processing
Warning: to set higher-precision angles.
Read CRYST1 info from PDB: a=62.134 b=62.134 c=62.134 alpha=109.47 beta=109.47 gamma=109.47
Setting active reference for distance-based masks: 'nat2_md-qm_0.pdb'
[strip :WAT,QMW,Na+]
Warning: Action specified before trajin/ensemble. Assuming trajin.
STRIP: Stripping atoms in mask [:WAT,QMW,Na+]
[crdaction nat2-0 cluster crdset nat2-0 dbscan minpoints 5 epsilon 0.9 sievetoframe rms :32,35,179&!.H= reference mass sieve 10 random out nat_clst-vs-t.dat summary nat_clst-sum.dat info nat_clst-info.dat cpopvtime nat_cpop-vs-t.agr normframe repout nat_rep repfmt pdb ]
Using set 'nat2-0'
----- nat2-0 (1-5250, 1) -----
'cluster': Command not found.
1 errors encountered reading input.
TIME: Total execution time: 5.4636 seconds.
Error: Error(s) occurred during execution.
Here is the input file:
#Load topology and trajectories
parm native2.parm
loadcrd nat2_md-qm.nc name nat2-0
loadcrd nat-ew2-0_mdqm.nc name nat2-0
loadcrd nat-ew2-0_mdqm1.nc name nat2-0
loadcrd nat-ew2-0_mdqm2.nc name nat2-0
loadcrd nat-ew2-0_mdqm3.nc name nat2-0
loadcrd nat-ew2-0_mdqm4.nc name nat2-0
loadcrd nat-ew2-0_mdqm5.nc name nat2-0
loadcrd nat-ew2-0_mdqm6.nc name nat2-0
loadcrd nat-ew2-0_mdqm7.nc name nat2-0
loadcrd nat-ew2-0_mdqm8.nc name nat2-0
loadcrd nat-ew2-0_mdqm9.nc name nat2-0
loadcrd nat-ew2-0_mdqm10.nc name nat2-0
loadcrd nat-ew2-0_mdqm11.nc name nat2-0
loadcrd nat-ew2-0_mdqm12.nc name nat2-0
loadcrd nat-ew2-0_mdqm13.nc name nat2-0
loadcrd nat-ew2-0_mdqm14.nc name nat2-0
loadcrd nat-ew2-0_mdqm15.nc name nat2-0
loadcrd nat-ew2-0_mdqm16.nc name nat2-0
loadcrd nat-ew2-0_mdqm17.nc name nat2-0
loadcrd nat-ew2-0_mdqm18.nc name nat2-0
loadcrd nat-ew2-0_mdqm19.nc name nat2-0
reference nat2_md-qm_0.pdb [ref]
strip :WAT,QMW,Na+
#Cluster analysis
crdaction nat2-0 cluster crdset nat2-0 \
dbscan minpoints 5 epsilon 0.9 sievetoframe \
rms :32,35,179&!.H= reference mass \
sieve 10 random \
out nat_clst-vs-t.dat \
summary nat_clst-sum.dat \
info nat_clst-info.dat \
cpopvtime nat_cpop-vs-t.agr normframe \
repout nat_rep repfmt pdb \
I wonder if it could be due to the fact that Amber & AmberTools 16 have been installed in serial only (?)
Also, as I’ve never run this kind of analysis, I wonder if there is any mistake in my input file?
Thanks for any suggestion,
Sincerely,
Ruth
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Received on Thu Nov 03 2016 - 09:30:03 PDT
