Here is an amber tutorial for clustering
https://amberhub.chpc.utah.edu/clustering-a-protein-trajectory/
Best Regards
Elvis
On Wed, 17 Jun 2020 at 09:13, Nada Afiva <nadaafiva.gmail.com> wrote:
> Thank you Sir,
> Please if you have example of an input to perform cluster analysis.
> Thank you.
>
> best regards,
> nadaafiva
>
> Pada tanggal Rab, 17 Jun 2020 pukul 10.37 Elvis Martis <
> elvis_bcp.elvismartis.in> menulis:
>
> > Hi
> > Averaging is not the same as cluster analysis.
> > In fact, average structure over 500 ns may not yield a physically
> > meaningful structure.
> > Instead, working with cluster representatives from largely populated
> > clusters would give you better understanding of the conformational
> > preferences.
> > Best Regards
> > Elvis
> >
> >
> >
> > On Wed, 17 Jun 2020 at 08:42, Nada Afiva <nadaafiva.gmail.com> wrote:
> >
> > > Dear Sir,
> > > Is it the same with cluster analysis?
> > >
> > > Thank you
> > >
> > > nadaafiva
> > >
> > > Pada tanggal Rab, 17 Jun 2020 pukul 03.02 Liao <liaojunzhuo.aliyun.com
> >
> > > menulis:
> > >
> > > > Yes, it is not hard to obtain the average structure, using cpptraj.
> > > > A sample script wth file name cpptraj.average.in will look like
> this:
> > > > -----------------------
> > > > #cpptraj -i cpptraj.average.in
> > > >
> > > > parm gasphase.prmtop [1]
> > > > parm reference.prmtop [2]
> > > >
> > > > trajin gastrajectory.mdcrd parm [1]
> > > >
> > > > autoimage
> > > > #read in reference
> > > >
> > > > reference reference.rst7 parm [2]
> > > > #compute rmsd and align the CA atom of residues 1-100 to the
> reference
> > > > crystal structure of the same molecule
> > > > #refer to p615 of AMBER 19 manual for atom syntax
> > > > rmsd rms1 reference :1-100.CA
> > > > average 500ns.aligned.pdb
> > > > ------------------------
> > > > Just run cpptraj -i cpptraj.average.in
> > > > and the generated pdb file will be your average structure
> > > >
> > > >
> > > > ------------------------------------------------------------------
> > > > Sender:Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
> > > > Sent At:2020 Jun. 16 (Tue.) 12:27
> > > > Recipient:AMBER Mailing List <amber.ambermd.org>
> > > > Subject:[AMBER] Average structure of production run
> > > >
> > > > Hello everyone,
> > > > I have run 500ns simulation of a ligand-G Quadruplex system, and now
> > need
> > > > to obtain the average structure of the run. Is it possible to obtain
> > one
> > > > such structure of this 500ns simulation? Is the input same as the one
> > we
> > > > use to obtain the pdb of a particular frame of the simulation?
> > > > Thank you
> > > >
> > > > Sruthi
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Received on Tue Jun 16 2020 - 21:30:02 PDT
