AMBER Archive (2009)

Subject: [AMBER] Ligand Diffusion Studies?

From: Jason A. Ford-Green (
Date: Thu Jan 15 2009 - 11:42:03 CST

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?

System Info:

Receptor Binding domain
~290 amino acids long
Possibly 2 active site gorges (each convoluted ~8-12 Angstroms
                               in length)

I know this is not saying much, but I hope it's still affective for conversation. Thank you for your time and consideration.

Jason Ford-Green

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