Re: [AMBER] binding energy of multiple ligand-receptor complex

From: <>
Date: Fri, 4 Dec 2009 04:47:26 -0500 (EST)

Hi all,

>> Now I am running MD simulation for multiple ligand-receptor complex
>> (such as 3-4 ligand bind 1 receptor to form one complex) and want to
>> calculate the binding energy. If it is single ligand - single receptor
> you can do several MM-PBSA calculations then.
> When you have a receptor with two ligands:
> Define calculation1 with ligand1 and receptor1 where ligand2 is part of
> the receptor.
> Then define calculation2 with ligand2 and receptor2 where ligand1 is part
> of the receptor.

Wouldnt that double-count the ligand-ligand interaction? I my opinion, you
would have to pick a sequence in which the ligands bind and then do MMPBSA
for R + L1, then R-L1 + L2, R-L1-L2 + L3 and so on. Additionally, if you
permute the sequence, you will get some info about (anti-)cooperativity of
binding and maybe an idea of the real order in which ligands bind...

Kind regards,

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

AMBER mailing list
Received on Fri Dec 04 2009 - 02:00:02 PST
Custom Search