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 - 21:00:04 PDT
