On Fri, Sep 22, 2017 at 11:10 AM, jacky zhao <jackyzhao010.gmail.com> wrote:
> 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
>
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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>
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Received on Fri Sep 22 2017 - 09:30:03 PDT
