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
