[AMBER] error in cluster analysis by cpptraj

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Thu, 12 May 2016 10:06:39 +0000

Dear Amber experts,

I need to conduct cluster analysis of several sequential MD trajectories

by inter atomic bond distance :111.OG, :164.NE2

I never used previously such analysis, so

cpptraj reported about ERROR.

I need your advise to identify error in my cpptraj.combined.cluster.in input file

that I ran by the command:

$ cpptraj -i cpptraj.combined.cluster.in

See details below.

Thank you,


cpptraj.combined.cluster.in file:

# Combined cluster analysis with cpptraj.

# Load topology and both trajectories
parm ../*.prmtop
trajin ../20_/prod4.mdcrd # 5000 frames
trajin ../21_/prod5.mdcrd # 5000 frames
trajin ../22_/prod6.mdcrd # 4971 frames
# Remove ions so they do not appear in output structures.
strip :WAT,Cl-,Na+,OL,PA,PE
# Cluster analysis command
# C1: Cluster output data set(s) name.
# dbscan: 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.
# rms <mask>: Use RMSD of atoms in <mask> as distance metric.
# sieve 20: Use <total> / 20 initial frames for clustering.
# out <file>: Write cluster number versus time to file.
# info <file>: Write detailed cluster results (including DBI, pSF etc) to file.
# summarysplit <file>: Write cluster information for split to file.
# splitframe 5000: Split clustering at frame 5000 (where first traj stops).
cluster C1 \
        dbscan minpoints 25 epsilon 0.9 sievetoframe \
        rms :111.OG, :164.NE2 \
        sieve 20 \
        out combined.cnumvtime.dat \
        info combined.info.dat \
        summarysplit split.dat splitframe 5000

The result:

$ cpptraj -i cpptraj.combined.cluster.in

CPPTRAJ: Trajectory Analysis. V15.00
    ___ ___ ___ ___
     | \/ | \/ | \/ |

| Date/time: 05/12/16 12:50:09
| Available memory: 170.02 MB

INPUT: Reading Input from file cpptraj.combined.cluster.in
  [parm ../*.prmtop]
        Reading '../mc.prmtop' as Amber Topology
  [trajin ../20_/prod4.mdcrd ]
        Reading '../20_/prod4.mdcrd' as Amber NetCDF
  [trajin ../21_/prod5.mdcrd ]
        Reading '../21_/prod5.mdcrd' as Amber NetCDF
  [trajin ../22_/prod6.mdcrd ]
        Reading '../22_/prod6.mdcrd' as Amber NetCDF
  [strip :WAT,Cl-,Na+,OL,PA,PE]
    STRIP: Stripping atoms in mask [:WAT,Cl-,Na+,OL,PA,PE]
  [cluster C1 dbscan minpoints 25 epsilon 0.9 sievetoframe rms :111.OG, :164.NE2 sieve 20 out combined.cnumvtime.dat info combined.info.dat summarysplit split.dat splitframe 5000]
    CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:111.OG,]) best-fit
                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.)
        Initial clustering sieve value is 20 frames.
        Cluster # vs time will be written to combined.cnumvtime.dat
        Cluster information will be written to combined.info.dat
        Summary comparing parts of trajectory data for clusters will be written to split.dat
                Frames will be split at: 5000
Error: [cluster] Not all arguments handled: [ :164.NE2 ]
        1 errors encountered reading input.
TIME: Total execution time: 0.1955 seconds.

Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
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Received on Thu May 12 2016 - 03:30:02 PDT
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