Hello amber users!
I am trying to perform clustering analysis using AMBER18 by following this tutorial:
https://amberhub.chpc.utah.edu/clustering-a-protein-trajectory/
But I am having difficulty determining the cluster size, could anyone advise how to do this.
My “analysis.in” file is:
###
parm ../../../stripped.1va3_solv.prmtop
trajin ../../../ensemble_nowat_100ns.nc
cluster c1 \
kmeans clusters 100 randompoint maxit 500 \
rms :
1-29.CA \
sieve 10 random \
out cnumvtime.dat \
summary summary.dat \
info info.dat \
cpopvtime cpopvtime.agr normframe \
repout rep repfmt pdb \
singlerepout singlerep.nc singlerepfmt netcdf \
avgout avg avgfmt pdb
run
###
Any help would be greatly appreciated! 😊
Kind regards,
Daniel.
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Received on Mon May 15 2023 - 08:00:02 PDT
