Dear Victor:
Thank you for your suggestion! Your suggestion worked perfectly! According to your suggestion and another friend Daniel, I modified my inputs and the cluster can works normally.Thank you very much ! Have a nice weekend! Best wishes.Hongyan Yu
发件人："Víctor Vargas" <victorbermudez00.gmail.com>
发送日期：2021-07-16 02:38:30
收件人：AMBER Mailing List <amber.ambermd.org>
主题：Re: [AMBER] [cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ]>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!
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jul 17 2021 - 01:30:02 PDT
