Hi everyone,
Recently, I am running cluster analysis of protein complex simulation.
But some errors occur. Could you give us some suggestions.
The total amino acids of the protein complex are 221.
We would like to perform rms :3-218.N,CA,C for cluster analysis.
Thank you for taking your time.
The input file were attached below:
# Load topology trajectory
parm ../wt_wat.parm7
trajin ../wt_wat_md_1ms.crd
# Remove ions so they do not appear in output structures.
strip :Na+,Cl- outprefix noions
# Cluster analysis command:
# C0: Cluster output data set(s) name.
# CLUSTERING OPTIONS:
# dbscan: Use the DBSCAN (density based) clustering algorithm.
# minpoints: Minimum # of points to form a cluster.
# epsilon: Distance cutoff for forming cluster.
# sievetoframe: Restore sieved frames by comparing to all cluster frames,
# not just centroid.
# DISTANCE METRIC OPTIONS:
# rms <mask>: Use RMSD of atoms in <mask> as distance metric.
# sieve 10 : Use <total> / 10 initial frames for clustering.
# OUTPUT OPTIONS:
# out <file>: Write cluster number versus time to file.
# summary <file>: Write overall clustering summary to file.
# info <file>: Write detailed cluster results (including DBI, pSF etc) to
file.
# cpopvtime <file> normframe: Write cluster population vs time to <file>,
# normalized by # frames.
# COORDINATE OUTPUT OPTIONS:
# repout <file prefix> repfmt pdb: Write cluster representatives to files
with
# PDB format.
# singlerepout <file> singlerepfmt netcdf: Write cluster representatives to
# single file with NetCDF format.
# avgout <file> avgfmt restart: Write average over all frames in each
cluster
# to separate files with Amber restart file
# format.
cluster C0 \
dbscan minpoints 25 epsilon 0.9 sievetoframe \
rms :3-218.N,CA,C
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
The error messages:
CPPTRAJ: Trajectory Analysis. V17.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 09/22/17 23:07:55
| Available memory: 2.932 GB
INPUT: Reading input from 'STDIN'
[parm ../wt_wat.parm7]
Reading '../wt_wat.parm7' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
[trajin ../wt_wat_md_1ms.crd]
Reading '../wt_wat_md_1ms.crd' as Amber NetCDF
[strip :Na+,Cl- outprefix noions]
STRIP: Stripping atoms in mask [:Na+,Cl-]
Stripped topology will be output with prefix 'noions'
[cluster C0 dbscan minpoints 25 epsilon 0.9 sievetoframe rms :3-218.N
,CA,C]
CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask
[:3-218.N,CA,C]) best-fit
DBSCAN:
Minimum pts to form cluster= 25
Cluster distance criterion= 0.900
Sieved frames will only be added back if they are within
0.900 of a frame in an existing cluster.
(This option is more accurate and will identify sieved
frames as noise but is slower.)
Pairwise distance data set is 'C0[PWD]'
Representative frames will be chosen by lowest cumulative distance to all
other frames.
[sieve 10 randomout cnumvtime.dat sil Silsummary summary.dat info
info.dat cpopvtime cpopvtime.agr normframe ]
Error: Missing or mismatched parentheses.
'sieve 10 randomout cnumvtime.dat sil Silsummary summary.dat info info.dat
cpopvtime cpopvtime.agr normframe ': Invalid command or expression.
1 errors encountered reading input.
TIME: Total execution time: 0.0672 seconds.
Error: Error(s) occurred during execution.
--
Lei Zhao, Ph.D.
International Joint Cancer Institute of the Second Military Medical
University
National Engineering Research Center for Antibody Medicine
New Library Building 11th floor,800 Xiang Yin Road
Shanghai 200433
P.R.China
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Received on Fri Sep 22 2017 - 08:30:04 PDT
