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

From: James Kress <>
Date: Mon, 25 Oct 2021 14:53:57 -0400

Why do you minimize the average structure? Won't that minimization just
result in another, non-average structure?


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-----Original Message-----
From: Adrian Roitberg <>
Sent: Monday, October 25, 2021 10:52 AM
Subject: Re: [AMBER] Does minimization require for average pdb structure
extract from 2drms plot using CPPTRAJ AMBER 16

Hi Priya

That script is not for a 2drms, it is just a simple 1D rmsd versus the
initial frame, and then the does average.

Once you get the average, yes, you need to minimize it. The process of
averaging can create some weird structures.

I would recommend a different path: Compute the average and THEN recalculate
the RMSD of the trajectory against the average pdb. Look for what frame is
closest to the average (lowest rmsd value), extract it, and minimize THAT


On 10/24/21 10:23 PM, priya murugan wrote:
> [External Email]
> Hi researcher,
> I'm really looking for your guidance and help in order for me to
> pursue my next step in computational work. I'm new to computational
> work and keen to learn more. 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
> I would be grateful for every suggestion that will be given to me.
> Thanks & Regards
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Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry Department of Chemistry
University of Florida
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Received on Mon Oct 25 2021 - 12:00:02 PDT
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