Re: [AMBER] RMSD-based clustering in CPPTRAJ/PTRAJ

From: Daniel Roe <>
Date: Fri, 20 Dec 2013 08:39:18 -0700


On Thu, Dec 19, 2013 at 10:53 PM, anu chandra <> wrote:

> center :1-293 mass origin
> image origin center

Just FYI this can now be done in one step with the 'autoimage' command -
see the manual for more details

> cluster :50-85,:265-280.CA,N,C,O mass clusters 10 out cluster_out
> averagelinkage gracecolor summary summary_out info Cluster_info repout
> centroid repfmt pdb
> **********************************************************************************************
> Unfortunately, when I align all the 10 cluster centroids I have seen that
> the position of helix-1 and helix-2 are not changed much as they align
> almost perfectly on top of the same from each of the centroid structure.

This is expected. Here you are explicitly specifying you want the best-fit
for residues 50-85 and 265-280. What I think you want to do is to perform
an RMS-fit on all atoms prior to clustering, then cluster on the helices
with the 'nofit' keyword, which will essentially give you the movement of
the helices with respect to the entire system, e.g.

rms first :1-293
cluster :50-85,:265-280.CA,N,C,O mass nofit ...

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Dec 20 2013 - 08:00:02 PST
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