[modeller_usage] Why should add ourself ligand in protein?

Dear modeller, I want to know what is the purpose of adding ligand in protein by ourself in Modeller, what will be the useful outcome that we can expect by adding ligand in our model in Modeller? I mean is there any routein in Modeller6v2 to study the active site or interaction of our added ligands and protein? Please let me know.

Yours truly, B.Nataraj

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