Is it possible to calculate the binding free energy using g_mmpbsa for protein complex? I have followed the tutorial but I could not create the files for two unbound protein and complex (dimer) protein.
The standard protocol for MMPB/SA calculations is as the following:
1) Molecular dynamics simulations of protein A in solvent (so, you will have a trajectory file for protein A);
2) Molecular dynamics simulations of protein B in solvent (so, you will have a trajectory file for protein B);
3) and molecular dynamics simulations of complex AB in solvent (so, you will have a trajectory file for complex AB);
Hence, you should have created these three files first, then run MMPB/SA code. You may also use an alternative protocol (with cost of not being able to measure the entropic change contribution on binding energy) by running only the simulations on the complex, and then saving from this trajectory separately the coordinates of only protein A and B, and so again creating three trajectory files, but with coordinates for A and B the same as their were in complex AB. To split protein A and protein B, you may also use VMD program.
Dear Sir, Thank you very much. I have a problem using g_mmpbsa. Because g_mmpbsa calculate BE at a oncel
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