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?
--- 08年12月29日，周一, Nathan Baker <firstname.lastname@example.org> 写道：
发件人: Nathan Baker <email@example.com>
主题: Re: [Apbs-users] absolute binding free energy
抄送: "apbs apbs" <firstname.lastname@example.org>
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?
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis