Hello Daniel,
Thank you for your suggestion! Your suggestion worked perfectly. I am using CPPTRAJ: Trajectory Analysis. V14.25Is the version too much low?My intent is using cluster to find the lowest energy structure according the distance data calculated from reweighting analysis.
According to your suggestion and another friend Victor，I am using the cpptraj version V18.01 and modified the input to :parm nanobody.prmtop
trajin 06_gamd_3.mdcrdcluster c1 \hieragglo epsilon 3.0 clusters 10 averagelinkage \rms :111.OG1,:113.H,:108.O,:111.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
It can calculate normally ！Thank you very much ! Have a nice weekend!
Best wishes.
Hongyan Yu
发件人：Daniel Roe <daniel.r.roe.gmail.com>
发送日期：2021-07-15 23:48:17
收件人：AMBER Mailing List <amber.ambermd.org>
主题：Re: [AMBER] [cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ]>Hi,
>
>What version of cpptraj are you using (i.e. what is the output of
>'cpptraj --version')?
>
>-Dan
>
>On Thu, Jul 15, 2021 at 3:03 AM 余鸿艳 <1915391047.st.gxu.edu.cn> wrote:
>>
>> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Jul 17 2021 - 01:30:02 PDT
