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?
_______________________________________________
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
Received on Wed Jan 29 2020 - 07:30:02 PST
