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. I have attached my 2drms plot for your reference.

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