MM/PBSA will calculate the these in a certain sense. It will
calculate all components of the energy for the protein, RNA, and
complex, as well as the differences (complex - receptor - ligand).
Thus, if you look at the differences for each of the energy terms
(only non-bonded terms are non-zero for MM/PBSA acting on a single
trajectory), this will give you the "interaction" energies for vdW,
EEL, and solvation terms (GB/PB, etc.).
Good luck!
Jason
On Fri, Jan 22, 2010 at 7:54 AM, qiaoyan <qiaoyan.dicp.ac.cn> wrote:
> Dear amber users:
> I have simulated three trajectories, a protein, a RNA and their complex, now I want to calculate the different compoents of their interaction energies, for example, nonbonded interaction energies, vdw energies, but I don't know how to do this? Could mmpbsa do this thing? Thank you for your kind help.
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Jan 22 2010 - 07:30:02 PST
