[AMBER] On the clustering of the ligand position within the cavity

From: James Starlight <jmsstarlight.gmail.com>
Date: Thu, 19 Mar 2015 16:50:12 +0100

Dear Amber users!

Using ptraj I've made clustering of the ligand position (specified by
:MOL) within the receptor's cavity using

trajin ../equil5.nc 100 999999999 1
center origin :1-291
center origin :MOL
image origin center
#fit the receptor
rms first :1-291.C,CA,N out rmsd_backbone_OR5P3_androstenone.dat
# don't fit the ligand
rms first :MOL out rmsd_ligand_OR5P3_allyl-phenyl-acetate.dat nofit
cluster out out_OR5P3_allyl-phenyl-acetate.dat representative pdb
average pdb means clusters 5 rms mass :MOL

as the result I've obtained some jump (~ 4 A) on the rmsd dat graph
calculated for the rms of ligand. However during the comparison of
the each structures from each representative clusters of this system
I've not found big difference between position of the ligand. Does it
means that method (rmsf mean) of clustering that I've used was not
enough sensitive for this task? What alternatives might be better


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Received on Thu Mar 19 2015 - 09:00:07 PDT
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