Minimization of PDBs for Ensemble NMAs

[Former user]

Hello Bio3D community, I was wondering if it is necessary to minimize the PDBs that I will be utilizing for my ensemble NMA. I was thinking about minimizing the PDB structures, then running NMA, however, if it is not necessary, I am thinking this could save me some time. Please feel free and let me know what is best!

Warm regards,

Daniel

[Xinqiu Yao]

Hi Daniel,

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It is not necessary. The methods bio3d provides are all structure based, which means they automatically use PDB structures as reference (minimal energy) points.

[Daniel Lim]

Thank you so much!