AMBER Archive (2008)

Subject: AMBER: For help: how to perform double decoupling thermodynamic integration calculation in AMBER10

From: yongleli (yongleli_at_itcc.nju.edu.cn)
Date: Mon Jul 07 2008 - 17:04:53 CDT

Dear Amber Users,

I am trying to calculate absolute binding free energy using termodynamic integration with double decoupling method(D. Hamelberg and J. A. McCammon, J. Am. Chem. Soc. 126, 7683, 2004). Assume A is a protein binding a ligand B,

A:B(sol)-------->A(sol)+B(gas) dG1

In my knowledge of AMBER, In TI calculation there are two prmtop files defining initiate state and final state. Here the final state seems to be a protein molecule in water and a ligand in vacuum. But I can only prepare a parmtop file containing a single protein in water. How can I deal with the ligand in gas phase?
 
I heve also resorted to some papers, just as(S. Wang et. al., J. Am. Chem. Soc. 128, 11830, 2006), and (P. Ren et. al., PNAS, 105, 6290, 2008), etc. but it seems to that authors did not mention this problem.

yongleli
2008-07-08

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