AMBER Archive (2006)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jul 24 2006 - 09:45:59 CDT

Dear Sangeeta,

> 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?

This is really an MMTSB question so you may have more joy checking their
website for a mailing list. However, I'll try and help as best I can. The
answer to your question is that I don't exactly know. At the time of writing
the tutorial it seemed a reasonable thing to do since in order to cluster
properly the structures will have to be rms fitted in some way so that the
rmsd from the cluster centroid can be accurately calculated. However, I
suspect that the kclust command in MMTSB actually performs an RMSD fit in
which case the previous fit is largely redundant. There is no guarantee of
this though and you should probably check the MMTSB documentation. That said
you can also easily check the results yourself. What happens if you take the
unfitted trajectory and pass it through the kclust command? Do you get
substantially different results?

All the best
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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