Dear AMBER users,
I am trying to do cluster analysis of a 4ns MD simulation of an rna.
I am following the tutorial 8 prepared by Ross Walker. I have some dooubts.
My simulation is in explicit solvent. Should I strip off the WATERS and IONs before saving pdb files of each frame?
What is the parametr radius used in the kclust command?.
Can we specify the number of clusters?
Thanks in advance
Mathew
/\/\athew
Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India
email mathew_kvarghese.yahoo.co.in
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Received on Wed Nov 23 2005 - 07:53:00 PST
