AMBER Archive (2006)

Subject: AMBER: kclust

From: Fabiana Caporuscio (andfadeout_at_hotmail.com)
Date: Wed Sep 27 2006 - 03:32:51 CDT

Dear All,
I would like to use MMTSB (kclust) to clusterize frames from a PMEMD
simulation as in the Ross Walker Tutorial 8 (section 6). I have tried to
write to the MMTSB list but they haven't answered me till now. I also read
the documentation about kclust on the MMTSB web page but I haven't found a
description of the options -cdist, -maxerr, -iterate and I also would like
to know the unit of measure of the radius (is the max RMSD between structure
in the same cluster?).
I have also another problem: I should perform the RMSD calculation just on
some selected residues but they are not continuous, in fact I should select
for example residue 7, 19, 29-35. I have found in the documentation about
lsqfit the option -l 10:21 to select from residue 10 to 21 but how can I
select for example the residues mentioned above? and if I select residues by
their numbers does the RMSD calculation consider also hydrogens? because I
would like to calculate the RMSD just on the heavy atoms of the selected
residues.
Thank you very much
Fabiana Caporuscio, PhD student
Department of Medicinal Chemistry
University of Siena

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