Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16

From: Hector A. Baldoni <>
Date: Mon, 25 Oct 2021 09:57:02 -0300

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.


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.
> 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
> _______________________________________________
> AMBER mailing list

  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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Received on Mon Oct 25 2021 - 06:00:02 PDT
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