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
Received on Fri Sep 22 2017 - 10:00:02 PDT
