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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Oct 18 2006 - 06:07:19 PDT
