Hello everyone!
I am interesting on host-guest inclusion complexes using quantum and molecular modeling technics. I ve done docking with vina software. Now i am intersting if i could do MM-PBSA calculations of my docking complexes ? i am confused if i should do molecular dynamics first or no just starting with my complexes pdb files obtaining with vina.
Any help or suggestions are recommanded. Thx so much.
H i Krid Adel
Have a look at below to see what you will need for carrying out MD simulation.
https://www.google.com.my/amp/s/www.researchgate.net/post/How_can_I_set_up_a_protein-ligand_complex_for_molecular_dynamics_using_NAMD/amp
HTH
Yes you can.
Check the link attached below:
Article Improving Docking Results via Reranking of Ensembles of Liga...
MM/PBSA calculations carried out on data obtained from MD trajectories is always reliable rather that static condition (docking). So it will be better to perform MD simulation for docked complex and then go for MM/PBSA using g_mmpbsa tool of gromacs.
You can go for MM-PBSA calculations after docking to evaluate the complex stability as it predict the accurate pose. There are number of papers explaining the importance of PBSA after docking. After that, you can go for dynamics calculations for the same pose and then you can again perform the PBSA calculations on the trajectories retrieved.
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