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!
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!
I have seen the trajectory. Ligand slowly detached from the protein and after few steps it reattached itself to some other place (other than the binding site).
I have seen the trajectory. Ligand slowly detached from the protein and after few steps it reattached itself to some other place (other than the binding site).
@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?
@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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VOTE
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!
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!
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VOTE
First, visualize the trajectory, for example using VMD.
First, visualize the trajectory, for example using VMD.
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VOTE
Dear Martin Klvana,
I have seen the trajectory. Ligand slowly detached from the protein and after few steps it reattached itself to some other place (other than the binding site).
Dear Martin Klvana,
I have seen the trajectory. Ligand slowly detached from the protein and after few steps it reattached itself to some other place (other than the binding site).
More
VOTE