Simulating a Binding Event

From: Alex Saad-Falcon (alexsaadfalcon_at_gmail.com)
Date: Tue Mar 06 2018 - 11:53:54 CST

Hello All,

I am fairly new to using NAMD and VMD for sophisticated simulations, but I
was just wondering about the general process to simulate a binding event
between a protein and a ligand. For example, I have this protein
https://www.rcsb.org/structure/3SZT in which the pdb file includes the
ligand (I believe). Do I need to move the ligand out of the protein but
close to the binding site, and then run NAMD?

Thanks for any feedback,

Alex

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