Hi everyone, 

I am studying a system composed by  a big size protein (Integrins family) complexed with small molecule candidates, trying to obtain a ranking of binding free energies. The receptor site is enough exposed and I suppose that the ligands (very flexible) could adopt different poses within the binding site.

I would like to approach these kind of systems by dynamics calculations: what about using GAMD for this task? I saw some references where the ligand binding is studied with GAMD (but the ligand start far away from the binding site, I would prefer to reduce the space within the supposed binding site).

Any suggestions and useful hints?

Thank you in advance

Andrea