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
algorithm?
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
run
quit
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Received on Fri Aug 29 2014 - 08:00:03 PDT
