Dear All,
I docked a ligand using Autodock vina and performed MD simulations for about 100ns.
I need help in analysis of the results. If we see the results can we say the ligand detached from the protein binding site and attached itself to some other site? If the ligand is detach can we say it is due to protein (unstable) on the basis of RMSD results?
1. Periodic boundary conditions were removed.
2. Protein structure was made using I-TASSAR (no PDB structure was available).
3. We we validate these results in wet lab.
4. Also please help in RMSD. What should be the criteria for selecting the best RMSD? Stable RMSD?
5. RMSD is Backbone least square fitting to heavy atoms of ligand.
6. RMSD of protein and ligand separate.
Really need help as I am totally new to MD simulations.
1. From the protein-ligand complex images and Hydrogen bond pattern, it is evident that the ligand was initially bound to the protein, then detached from the protein and, again made H-bonds with the protein for last ~20 ns.
2. It is recommended to run reasonably long MD Simulations (500 ns maybe) to check the stability of the protein-ligand complex. 100 ns is not enough!
@sutanu mukhopadhyay thank you so much for the answer. I will perform md simulation for another 100ns now.
Can you please recommend any books or articles where I can learn md simulation in detail especially about RMSD?
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