I have (series of) two different MD trajectories of protein-ligand complex. In complex-I, the ligand was docked with the protein manually, however in complex-II, the docking was performed in AutoDock. After that MD simulation (in Gromacs) was performed for 50ns. To detect the better complex, I already analyzed the RMSD, Rg, RMSD of ligand and even performed the ligand protein interaction. However, doing all these analysis, I am not even able to find the better trajectory. Please help in this context.
Hello.
There is no such thing as "better" trajectory. What you have are two independent MD simulations that sampled protein-ligand interactions. Therefore, results from both trajectories are valid, especially if both converged to a similar point.
My advise is for you to use g_mmpbsa in order to determine free energies of binding for both simulations and to choose the one with lowest binding energy (theoretically, the most stable). But also evaluate the evolution of binding energies on the other to see if it reached a similar binding energy as the better one (simply it may need more time to get there!)
Ricardo
Hello.
There is no such thing as "better" trajectory. What you have are two independent MD simulations that sampled protein-ligand interactions. Therefore, results from both trajectories are valid, especially if both converged to a similar point.
My advise is for you to use g_mmpbsa in order to determine free energies of binding for both simulations and to choose the one with lowest binding energy (theoretically, the most stable). But also evaluate the evolution of binding energies on the other to see if it reached a similar binding energy as the better one (simply it may need more time to get there!)
Ricardo
Hello!
In addition to what Ricardo J Ferreira said, you may consider the cluster analysis to extract the most representative structure from the simulation. Although the most representative might not always be the best structure, the cluster analysis gives you a visual description of the "most explored" conformations.
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