[gmx-users] extraction of PDB from clusters.pdb

Shine A shine.a at iisertvm.ac.in
Wed Jul 17 06:57:56 CEST 2013


        Using g_cluster I clustered snapshots in md trajectory using the
command as follows

g_cluster -s sd_7.tpr -f traj7.trr -dist rmsd-distribution.xvg -o
clusters.xpm -sz cluster-sizes.xvg -tr cluster-transitions.xpm -ntr
cluster-transitions.xvg -clid cluster-id-over-time.xvg -cl clusters.pdb
-cutoff 0.25 -method gromos -dt 10

Here I got clusters.pdb having central structures in each cluster. Is there
any command line option available to extract all individual files from

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