Preparation of the receptor

[Rocío Riveros]

Dear Jacob,
I know that un the tutorial says: "Remove all ligands, water, or non-protein atoms. This can be done in a PDB viewer such as Pymol or VMD". But in my case, the protein has a molecule of FAD that is fixed to the protein through H-Bonds, so I considered to let the cofactor stay at the structure. It will affect the proccess? Can you give me some advice?
Thanks

[Jacob Durrant]

Hi Rocío. I think you should be fine including the FAD molecule as if it were part of the receptor. I’m assuming that you’re using AutoGrow with AutoDock Vina. My understanding it that Vina can handle receptors that include cofactors: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-October/010387.html

Take care.

[Author]

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