=.=! oops
Got it
Thanks a lot.
2017-09-23 0:36 GMT+08:00 Daniel Roe <daniel.r.roe.gmail.com>:
> You are missing a backslash after your 'rms' keyword in your 'cluster'
> command, causing 'sieve' and all subsequent options to be treated as a
> separate command. Add a backslash after the 'rms' part.
>
> -Dan
>
> On Fri, Sep 22, 2017 at 12:13 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 18:30:02 PDT
