AMBER Archive (2009)
Subject: [AMBER] Ligand Diffusion Studies?
From: Jason A. Ford-Green (jgreen_at_ccmsi.us)
To Whom it May Concern,
My question simply is can anyone suggest a viable set of approaches for ligand diffusion/migration simulations? Currently I am making a concerted effort with GB Solvent REMD, and Hybrid Solvent REMD with the ligand inside previously defined gorges to the active site. It remains to be seen if this approach works. I've seen some literature regarding essential dynamics, force-probe, and random expulsion molecular dynamics simulations. Any experienced-based thoughts on the matter?
Receptor Binding domain
I know this is not saying much, but I hope it's still affective for conversation. Thank you for your time and consideration.