Hello Daniel,
Thank you for writing letter in reply and providing newest cpptraj version for me!
Wish you have a good weekend!
hongyanYu
发件人：Daniel Roe <daniel.r.roe.gmail.com>
发送日期：2021-07-21 00:12:44
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,
>
>On Sat, Jul 17, 2021 at 4:01 AM 余鸿艳 <1915391047.st.gxu.edu.cn> wrote:
>>
>> Hello Daniel,
>> Thank you for your suggestion! Your suggestion worked perfectly. I am using CPPTRAJ: Trajectory Analysis. V14.25Is the version too much low?
>
>Yes - that version is before the cluster silhouette calculation was
>introduced (also it's about 7 years old!). I always recommend using
>the latest version from either AmberTools or direct from GitHub:
>https://github.com/Amber-MD/cpptraj
>
>Note that when cpptraj started being developed primarily on GitHub, I
>moved from the old AmberTools versioning scheme with 2 numbers
>(<AmberToolsVersion>.<patch>) to an internal versioning scheme with 3
>numbers (<major>.<minor>.<revision>). So the more recent versions of
>cpptraj are numbered <major>.<minor>.<revision>.
>
>-Dan
>
>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
>>
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>> 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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>> >
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>>
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Received on Thu Jul 22 2021 - 19:00:02 PDT
