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 - 20:30:04 PDT
