Thank you very much Dr Hector. I would definitely consider your suggestion.
Thanks for time and gratefully received.
On Mon, 25 Oct 2021, 20:57 Hector A. Baldoni, <hbaldoni.unsl.edu.ar> wrote:
> Hi Priya,
> In my opinion, an average structure is not a real dynamic structure but
> a construction. I think that a more appropriate procedure would be to
> cluster the trajectory is five or ten leaders and perform 2drmsd
> between them. this would allow you to ensure that such leaders exist in
> the trajectory and that a given number of conformations are represented
> by them. Maybe someone may have a better opinion on the subject.
>
> Greeting,
> Hector.
>
>
> El 2021-10-25 00:27, priya murugan escribió:
> > Hi researcher,
> >
> > I'm really looking for your guidance and help in order for me to pursue
> > my
> > next step in computational work. Currently, I'm using AMBER 16 to do
> > Molecular Dynamic (MD) simulation and trajectory analysis. The protein
> > I'm
> > working with is 5IBE. I used CPPTRAJ to extract RMSD'd PDB's from
> > trajectories. I extract specific frames of the trajectory in a 2drms
> > plot,
> > to generate the average structure in PDB format. This is the script I
> > used
> > to generate the average PDB structure from a 2drms plot.
> >
> > cpptraj.in file
> > trajin 5IBE_heme_md_pc.binpos 2100 2500
> > rms first mass .C,CA,N
> > average 5IBE_heme_md_pc_2100-2500.pdb pdb
> >
> > 2100-2500 is the frame value from the 2drms plot.
> >
> > My question is do I need to minimize the average PDB structure that I
> > got
> > from CPPTRAJ analysis before continuing with molecular docking? Is that
> > ok
> > If I continue using this average PDB structure for the docking process
> > without minimization? Please let me know, I need some clarification.
> >
> > I would be grateful for every suggestion that will be given to me.
> >
> >
> > Thanks & Regards
> > *PRIYA MURUGAN *
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> --------------------------------------
> Dr. Hector A. Baldoni
> Profesor Titular (FQByF-UNSL)
> Investigador Adjunto (IMASL-CONICET)
> Area de Quimica General e Inorganica
> Universidad Nacional de San Luis
> Chacabuco 917 (D5700BWS)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.:+54-(0)266-4520300 ext. 6157
> --------------------------------------
> First things first. But not necessarily in such order.
>
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>
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Received on Mon Oct 25 2021 - 07:00:02 PDT
