AMBER: Does clustering involve fitting?

From: Steve Spronk <>
Date: Fri, 25 Jul 2008 16:02:09 -0400

Hello all,


The clustering utility of ptraj involves an RMSD calculation. In performing
this calculation, are the two structures fit in order to determine the RMSD,
or are the coordinates just used as they are read in? I'm interested to
know because we'd like to use the rms command to fit the whole protein, but
then cluster the resulting structures (without re-fitting) by measuring the
RMSD values of just a single loop. But I'm concerned that the cluster
command itself will re-fit the structures by overlaying the atoms of the
loop. If this re-fitting is the case, is there an option to turn it off?
I'd appreciate some clarification on this issue.




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Received on Sun Jul 27 2008 - 06:07:56 PDT
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