AMBER Archive (2006)

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

From: sangeeta (sangeeta_at_bioinfo.ernet.in)
Date: Wed Jul 26 2006 - 08:42:47 CDT

Dear Dr. Ross,
Thanks for your inputs. I have checked the MMTSB documentation but there
is nothing mentioned about the pre-fitting of frames (to be clustered).
I am experimenting with the pre-fitted and non-pre-fitted clustering as
you have suggested.
Thanks a lot.
Sangeeta
> 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
>
> /\
> \/
> |\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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