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

From: Daniel Roe <>
Date: Fri, 20 Mar 2015 08:14:48 -0600


On Thu, Mar 19, 2015 at 9:50 AM, James Starlight <> wrote:
> trajin ../ 100 999999999 1
> center origin :1-291
> center origin :MOL
> image origin center

My guess is that 'autoimage' from cpptraj would do a better job than
these commands. Imaging artifacts could be why you are seeing
transient jumps in your RMSD.

> cluster out out_OR5P3_allyl-phenyl-acetate.dat representative pdb
> average pdb means clusters 5 rms mass :MOL

I think the rms distance metric in ptraj clustering is *always*
best-fit, so all you are doing here is clustering based on internal
changes in MOL, which is not what you want I think. You can do this in
cpptraj by first RMS-fitting on your protein, then clustering with
'nofit', something like e.g.

rms first :1-291.C,CA,N
cluster C0 out cnumvtime.dat summary summary.dat info info.dat \
  rms mass nofit :MOL clusters 5 \
  clusterout cluster clusterfmt netcdf \
  repout representative repfmt pdb


PS - You may also want to strip any water/ions in your system prior to
autoimage as well.

> 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
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Mar 20 2015 - 07:30:02 PDT
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