The best initial structure of Protein-Protein complex

From: Alireza Mansouri (
Date: Mon Feb 24 2020 - 03:54:21 CST

Dear NAMD users,

I would like to research on the interaction betweentwo proteins using MD Simulation. However, I do not know what the best way isto obtain the initial structure of protein/protein complex before simulation.As far as I know, there are some docking web servers and software like Hex8,which can be used for this work. I did some docking simulations and found thateach software or server provided different result (different proteins orientation).

Can anyone please offer me some advice?

Can I use the result of Hex 8 for my MD Simulation?
Thanks in advance Alireza


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