AMBER Archive (2006)

Subject: AMBER: Tutorial 8, section 6: best fit before clustering

From: sangeeta (
Date: Mon Jul 24 2006 - 08:18:05 CDT

Dear Amber users,
I have a query related to the AMBER Tutorial 8, section 6 of the TRPCage
simulation, where cluster analysis is used. In this tutorial, before using
kclust of MMTSB, all the MD trajectory conformations are best fitted to
the helix of the NMR structure and then the PDB files are generated. My
question is, is it essential to have the frames from MD in the same
orientation (best fitted to a reference structure) before using kclust?

Thanks and best wishes,
Sangeeta Sawant
Bioinformatics Centre
University of Pune
Pune - India

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