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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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >_______________________________________________
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>
>
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Received on Tue Jul 20 2021 - 09:30:02 PDT
