[AMBER] clustering problem in ambertool14

From: Mahendra B Thapa <thapamb.mail.uc.edu>
Date: Tue, 16 Dec 2014 13:28:13 -0500

Dear Amber users
I used following command for clustering 50ns all-atom simulated data.
cpptraj -i input_file -p para_top
where 'input_file' consists of

trajin mdcrd_files
autoimage
rms first mass .C,CA,N
strip :Na+,WAT
cluster :1-291.CA,N,C,O mass clusters 10 out cluster_out nofit
averagelinkage \
summary summary_out info Cluster_info repout box2.rep repfmt pdb
clusterout cluster.nc clusterfmt netcdf
go

After running the command, I got following message without any output files:

1]terminate called after throwing an instance of 'std::bad_alloc'
  what(): std::bad_alloc
Aborted

2] Warning: One or more analyses requested creation of default COORDS
DataSet.
    CREATECRD: Saving coordinates from Top to file to "_DEFAULTCRD_"


3]Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning: after the RMS-fit is performed.

Any comments and suggestion will be very useful.

Thank you,
Mahendra Thapa
University of Cincinnati
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Received on Tue Dec 16 2014 - 10:30:04 PST
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