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

From: priya murugan <priyajenny712.gmail.com>
Date: Mon, 25 Oct 2021 10:23:06 +0800

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.

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

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Received on Sun Oct 24 2021 - 19:30:02 PDT
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