[gmx-users] Residue Selection

[Michael Carter]

Hi,

Not to worry. I have create the rmsd matrix using g_rms and this allows
you to then write the entire protein to the clusters.pdb with the RMSD of
the binding site residues being used.

Mike





On 18/11/2014 09:15, "Michael Carter" <Michael.Carter at icr.ac.uk> wrote:

>Hi,
>
>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.
>
>Thanks
>
>Michael Carter
>
>
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