Dear all,
I have about 1500 conformers which were generated by a docking calculation of a ligand. These conformers were distributed at different positions in the active site of the receptor. And I used ptraj to do cluster analysis for these conformers. But when I checked the results of the cluster analysis, I found that all the 1500 conformers were about at the same position. I inferred that cluster analysis does alignment first and then groups conformers . So I wander if cluster analysis does really do alignment firstly ? and if it does , is there anyway to turn off the "do alignment" option ?
Here is the trajin file:
trajin ligand1.pdb
trajin ligand2.pdb
trajin ligand3.pdb
.....
trajin ligand1490.pdb
cluster out ligand representative pdb average pdb all pdb averagelinkage clusters 8 rms mass
Many thanks for your help
Bin Sun
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Received on Thu Dec 20 2012 - 01:00:03 PST
