James,
My guess to your RMS jump is there's a change in your trajectory that's
being swallowed up or cutoff in your clusters so you're not seeing it. I'd
go and check the trajectory itself after centering to see if something
weird is happening, which should give an idea.
You can also try adding in 'nofit' into the clustering command, since I
think it might do an RMS fit again to your ligand and override your
previous RMS fit, but I'm not sure on that count.
To answer your second set of questions-
You can specify RMS cutoff with epsilon #- it replaces the clusters command
in the script, where you can specify the RMS cutoff as # of angstroms.
Clustering just produces a set limit of clusters, though I'm hazy on how
the RMS for those are calculated.
For your second question, assuming I'm interpreting it correctly, yes, you
can fit a stripped trajectory to a corresponding reference. It's probably
best to have a reference structure that would correspond to the stripped
trajectory, ie a stripped pdb file, starting frame/structure, etc.
Best,
Kenneth
On Thursday, March 19, 2015, James Starlight <jmsstarlight.gmail.com> wrote:
> 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?
>
> Thanks!
>
> James
>
> 2015-03-19 16:50 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
> > 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
> > here?
> >
> > James
>
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Received on Thu Mar 19 2015 - 10:30:03 PDT
