[AMBER] Obtaining representative structures from clustering

From: Jonathan Gough <jonathan.d.gough.gmail.com>
Date: Fri, 29 Aug 2014 10:56:06 -0400

Hi All,

Sorry if this is a simple question. Essentially I am looking for how to
generate a representative structure from a clustering calculation. What I
understand is as follows.

When running a cluster command, the output lists a "representative frames"
for each cluster. I am guessing that I could use that number and the
origional trajectories to generate a .rst file and therefore a .pdb.
   If so, how does one (what is the best way to) do that (especially if I
have more than one trajectory as the input)?

In looking through the manual (section 28.13.1) I now see two commands that
might have performed the task for me when I ran the calculation
(singlereoout and repout)
   Can someone provide some insight on their use and the difference between
the two?
   Also, can these commands be used after a clustering calculation has been
performed (eg. saving the processing time of re-running the clustering

If it's helpful - here are the cpptraj commands I used to generate my
clustering results.

parm nowat.dimer.prmtop
trajin prod01-24-dimer.nc
trajin prod25-30-dimer.nc
cluster C1 :1-164 clusters 10 sieve 10 epsilon 4.0 out cnumvtime.dat
summary avg.summary.dat clusterout cl clusterfmt netcrd
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Received on Fri Aug 29 2014 - 08:00:03 PDT
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