AMBER Archive (2009)

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

From: Oliver Kuhn (oak.amber_at_web.de)
Date: Fri Dec 04 2009 - 03:10:39 CST

> -----Urspr黱gliche Nachricht-----
> Von: "欧阳德方" <ouyangdf1978_at_hotmail.com>
> Gesendet: 03.12.09 11:55:53
> An: <amber_at_ambermd.org>
> Betreff: [AMBER] binding energy of multiple ligand-receptor complex

>
> Dear 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 complex, we can use MM-PBSA method. However, I have no idea how to calculate binding energy of several ligand - single receptor complex. It is very appreciated if you can give me some ideas.
>
> Merry Christmas!
>
> Regards,
> Ouyang

Ouyang,

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.
... and so on for more ligands.

Good luck!
Oliver

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