[gmx-users] Residue Selection

Michael Carter Michael.Carter at icr.ac.uk
Tue Nov 18 10:15:51 CET 2014


I have made and I have then clustered my results based upon this selection of residues.

This was performed like this:

g_cluster -f protein_nojump_rt.xtc -s protein.tpr -n index.ndx -o rmsd-clust.xpm -g cluster.log -dist rmsd-dist.xvg -ev rmsd-eig.xvg -sz clust-size.xvg -tr clust-trans.xpm -ntr clust-trans.xvg -clid clust-id.xvg -cl clusters.pdb -method gromos -cutoff 0.1

Is there a way to do this but also print out the remaining protein to the resultant clusters.pdb? As currently this file includes only the binding site residues in index.ndx.


Michael Carter

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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