Dear Amber users,
I am trying to run cpptraj for cluster analysis
Script that I am following is
parm nanobody.prmtop
trajin 06_gamd_3.mdcrd
cluster c1 \
hieragglo epsilon 3.0 clusters 10 \
averagelinkage \
rms :111.OG1,:113.H \
sieve 10 random \
out cnumvtime.dat \
sil Sil \
summary summary.dat \
info info.dat \
cpopvtime cpopvtime.agr normframe \
repout rep repfmt pdb \
singlerepout singlerep.nc singlerepfmt netcdf \
avgout Avg avgfmt restart
All the time I am getting an error
Error: [cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ]
When I keep the process running ，it can output nine structure but during the process will appear warning
Too many iterations in routine! Convergence failed
I don't know how to deal with this error. Please help me!
Your kind help will be highly appreciated!
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Received on Thu Jul 15 2021 - 00:30:02 PDT
