[AMBER] How to add restraints to a ligand correctly while decoupling it from complex?

From: wliu <wliu.itcs.ecnu.edu.cn>
Date: Mon, 02 Nov 2015 20:56:29 +0800

Dear all,

   I am trying to use double decoupling method to calculate absolute
binding free energy of a protein-ligand complex. According to this
method, ligand need to be decoupled from solvent and complex
respectively. I have already decoupled the ligand from solvent. After
that, I want to decouple the restrained ligand from complex using
Thermodynamic Integration in Amber. To keep ligand from moving out while
decoupling, restraints should be add on it correctly. So any advice?
Have someone done this before?

Thanks in advance.

Wei Liu

AMBER mailing list
Received on Mon Nov 02 2015 - 05:00:08 PST
Custom Search