Hello everyone. I am working with peptides of around 9 amino acids and I am going to do a molecular docking with them. But first I need to get them the 3D peptide structures. I plan to work with AMBER and built linear peptides using Xleap, but now I would like to minimize and optimize them. However, I don't know what conditions to use and I need to know if the methodology is correct. Thanks for your recommendations and suggestions.

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