Try the next changes:
1) Erase the backslash \ between
hieragglo epsilon 3.0 clusters 10 *\*
averagelinkage
hieragglo epsilon 3.0 clusters 10 averagelinkage \
2) Change: sil Sil \
to: sil sil /
(I have not used the argument "sil", but the change could work)
3) Change: avgout Avg avgfmt restart
to: avgout avg avgfmt restart
Be careful with using capital letters. They could be "not valid arguments"
El jue, 15 jul 2021 a las 0:03, 余鸿艳 (<
1915391047.st.gxu.edu.cn>) escribió:
> 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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>
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Received on Thu Jul 15 2021 - 12:00:02 PDT
