thanks a lot.
On Wed, Jan 29, 2020 at 7:14 AM Thayer, Kelly <kthayer.wesleyan.edu> wrote:
> If you are running cpptraj to perform clustering on an MD trajectory, you
> will get files called centroid.cn.pdb where n is an index beginning at 0 up
> to the number of clusters you have. These represent the pdb files of the
> centroids of your clusters.
>
> Below is a snippet of BASH code from my wrapper script that generates the
> input for multiple cpptraj runs over a range of number of clusters.
>
> I hope you find this helpful!
> best regards,
> Kelly Thayer
>
> # STEP 1. Generate the input file to cpptraj directing k-means clustering
>
> for NCLUST in $(seq 2 $MAXCLUST); do
>
> cat <<EOF> ${SAMPLENAME}_kclust$NCLUST-cpptraj.in
> # cluster analysis with cpptraj
>
> # Load stripped topology file
> parm ../${SAMPLENAME}_strip.prmtop
>
> # Reference file for aligning snapshots
> reference ../${SAMPLENAME}_strip.inpcrd
> # Load stripped trajectory file
> trajin ../${SAMPLENAME}_1-100_strip.trj
>
> # Align all the snapshots on the reference structure
> rms reference $STARTRES-$ENDRES
>
> # Cluster with k-means
> cluster kmeans :$STARTRES-$ENDRES mass clusters $NCLUST maxit
> 1000 out cluster_out averagelinkage gracec\
> olor summary summary_out info cluster_info repout centroid repfmt pdb
> clusterout cluster.nc clusterfmt n\
> etcdf
>
> EOF
> done
> ________________________________
> From: Lod King <lodking407.gmail.com>
> Sent: Tuesday, January 21, 2020 10:16 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] cpptraj_clucster
>
> HI AMBER
>
> Is there any example with command to extract cluster and output with pdb
> using cpptraj?
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Received on Sat Feb 01 2020 - 11:00:02 PST
