AMBER Archive (2006)

Subject: AMBER: modeling of ligand concentrations

From: Sean Rathlef (sean_at_syncitium.net)
Date: Mon Oct 16 2006 - 15:43:51 CDT

Folks,

I have a ligand (L) and a receptor (R). I am forming a complex LR, and want to model this in NPT. The energy levels of L + R and also of complex RL is going to depend on the standard state selection of [L]. Hence, if I model a single molecule of L and a single molecule or R, the relative energy will not take into consideration the concentration of L.

Does anyone know how I could model my complex using a specific concetration of L? An explicit model would be too complex. I have considered using a dielectric representation of solvated L (by mass percentage in water), but this leads to very subtle shifts in modeled dielectric, and I fear is not representative of the system in question.

Does anyone have a better suggestion?

Sean

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