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

From: Dr. Anselm Horn <>
Date: Mon, 25 Oct 2021 11:32:36 +0200


please note that an averaged pdb file may contain an unnatural structure
due to averaging e.g. two conformational side chain minima into an
high-energetic transistion state-like structure. Thus, it is not well
suited as a structure representative of your MD simulation.

An alternative would be to use clustering of that (part of the)
trajectory you are interested in, and then use the most populated
cluster representative structure for your further workflow.
Clustering is also implemented in cpptraj, and therefore ready for your
use (see the comprehensive Amber manual).

Whether a minimization is needed before docking, others may know better.
Personally, I'd do a short relaxation (= minimization) of the structure.
The best way IMHO, however, would be to look for published papers that
did MD with subsequent docking to see what exact workflow they used.



Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)

Am 25.10.2021 um 05:27 schrieb priya murugan:
> 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
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Received on Mon Oct 25 2021 - 03:00:02 PDT
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