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 - 21:00:03 PDT
