I am using the VMD plugin QwikMD to do MD simulations of my protein-protein complexes. Hereafter I am using the NAMD2 analysis to calculate my total energy of the system along with all of the other energies. I want to find out whether my reasoning is correct: If I have protein A, B and the complex AB, would it be correct to take the interaction energy as the average total energy of each separate simulation and have Binding energy = energyAB - energyA - energyB? I am also doing a simulation in the presence of metal and without metal where binding energy would be BE = MetalBound - MetalFree. Is this the correct approach for a simple estimate of binding energy?
Protein-protein binding is like protein-ligand binding: a solvent substitution event. i would consider only non-bonded (electrostatic and non-electrostatic) interaction energies.
Your approach mostly gives the interaction energy between them. Of course, interaction energy is also part of binding free energy. To obtain correct binding free energy use MM-GBSA or MM-PBSA method. The following links are useful in writing a configuration file for NAMD2 to calculate binding free energy.
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2015-2016/2058.html
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/2726.html
I hope it helps
Beware MM-GBSA, MM-PBSA:
Article Absolute Binding Free Energy Calculations: On the Accuracy o...
You can use MolAICal ( https://molaical.github.io) to calculate the MM/GBSA based on the simulated results of NAMD2. Please see the tutorial: MM/GBSA tutorial by NAMD and MolAICal in the website: https://molaical.github.io/tutorial.html
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