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

From: James Starlight <>
Date: Thu, 19 Mar 2015 17:30:57 +0100

Just to add some points:

1) is it possible in addition to specify rmsd cut-off or threshold for
each clustering step?
2) is it possible to strip all solvent from the system prior to the
rmsf fit and clustering to obtain its stripped cluster.pdb as well as
its corresponded representative structures?



2015-03-19 16:50 GMT+01:00 James Starlight <>:
> Dear Amber users!
> Using ptraj I've made clustering of the ligand position (specified by
> :MOL) within the receptor's cavity using
> trajin ../ 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
> here?
> James

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Received on Thu Mar 19 2015 - 10:00:02 PDT
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