I'm using ptraj to cluster a trajectory using only the coordinates of a
ligand in a protein/ligand system.
Everything runs smoothly, but the coordinates written out for each
cluster appear to be transformed (although there is nothing in the
ptraj/cluster documentation about this). Is there a way to get the
clustered coordinated reported in the original coordinate system?
Here's the ptraj script I'm running (Amber10):
ptraj protein_ligand_system.top << EOF
trajin protein_ligand_system.trj
cluster out testcluster representative pdb all pdb averagelinkage
clusters 5 rms :LIG & !.H=
EOF
Thanks,
Paul Beroza
Elan Pharmaceuticals
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Received on Fri May 07 2010 - 09:00:03 PDT
