Hello everyone,
If I want to get the relative binding free energy of the ligand--protein complex, what should I do to use the APBS to compute it?
Thank you,

--- 08年12月29日,周一, Nathan Baker <baker@biochem.wustl.edu> 写道:
发件人: Nathan Baker <baker@biochem.wustl.edu>
主题: Re: [Apbs-users] absolute binding free energy
收件人: youpan20032003@yahoo.com.cn
抄送: "apbs apbs" <apbs-users@lists.sourceforge.net>
日期: 2008,1229,周一,6:39上午

Hello --

I would not recommend using implicit solvent models to calculate absolute binding free energies; they are best suited to the calculation of relative binding free energies.  In fact, the calculation of absolute binding free energy is challenging with nearly any computational method currently available.

Can you pose your problem as a relative binding free energy calculation instead?



2008/12/27 有盼 缪 <youpan20032003@yahoo.com.cn>
Dear ,
I use GROMACS to study a complex and I want to get the absolute binding free energy of the ligand binding to the protein. In the APBS's Documentation, there are several examples to do with the binding energy, but they are different greatly, so how should I compute the binding free energy?
Thank you,


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Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/