I have used QwikMD/NAMD to run a simulation of a system containing two protein chains, and I would like to calculate the free energy of the binding interaction. How would I go about doing this?
One method I have heard of is MM/PBSA, but I am not sure how to actually implement this method to calculate the free binding energy from my simulation results. Is there software that can be used to automatically calculate the free binding energy from a QwikMD/NAMD simulation? Is there anything specific I need to do in the simulation setup to calculate this value? Any detailed tutorials that I can follow?
Thank you for any recommendations!
1. https://github.com/aspitaleri/gmxpbsa
2. https://valdes-tresanco-ms.github.io/gmx_MMPBSA/versus/
Instead of gmx_based methods that require the trajectory to be in gmx format, use amber related tools:
https://ambermd.org/tutorials/
https://ambermd.org/tutorials/advanced/tutorial3/
The 2nd link refers to prot-prot binding free energy calculation.
The amber can read the NAMD trajectory so you don't need to convert. You may need to create topology for this, and for that you can use ~ParmED.
Good luck.
In a simple way, you can use the HAWKDOCK server for the calculation of protein-protein complex interaction energy via MM-GBSA (http://cadd.zju.edu.cn/hawkdock/)
You can follow this as well: https://doi.org/10.3389/fcell.2020.611503
Is the HAWDOCK sever calculation as accurate as calculating the free energy directly from an MD simulation? I am interested in calculating the free energy for the protein-protein complex directly from my NAMD simulation, but I am struggling to do so.
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