AMBER Archive (2009)

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

From: steinbrt_at_rci.rutgers.edu
Date: Fri Dec 04 2009 - 03:47:26 CST

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

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