I have simulated a complex ( A protein docked with two ligands), and the ligands are bind to two different protein sites. Still, from the start of the simulation, ligands are positioned in other sites of the protein. I have tried various methods to see this substitution, for example, by lowering the time step to 0.01 fs; however, it didn't work. I will be thankful if you know any methods for this regard.
Can you share the initial structure used for the simulation and the first snapshot from the simulation?
Change the desired sites in times of docking. Run the docking complex in MD simulation. So, You have an initial specific site's binding ligand.
Thank you Sourav, I did so. At first, I'd docked two ligands to the protein; then, I used it as an initial structure for MD simulation. But from the first frame, it shows me different binding sites for each ligand.
Thank you Martin Klvana
Since this project is not related only to me, I don't have permission to share it. If you know any methods for this issue, I will appreciate it.
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