I have a sensor which can show its sensing towards cu+ ion. I wanted to study their interaction computationally using some docking methods. Can any one help me in finding a way to do this.
Thank you for answering my question! Can you a bit elaborate the technique. It would be a great help if you can send me a reference!
Based on interactions like hydrogen bonds, hydrophobic, vander Waals etc in Schrodinger, Commercial software package where Glide, a docking tool can be used to perform and visualize the interactions between the ion with ligand or aminoacids of a protein.
You may try to make a ligand-substrate structure and perform complete optimization of geometry with the charge in the ion using QM methods. The software SPARTAN has a provision to do it.
Best of luck
You may want to search "Molecular Dynamics" instead of "Molecular Docking".
As Dr. Apurba already suggested QM methods might also be best.
However, if your sensor is quite large to perform QM.
There's also this methods called QM/MM, Mixing QM with MM to reduce calculation demands into manageable level :)
I think Dr. Kim's suggestion of QM/MM for large systems should work. Please try as Dr. Kim suggested. Best.
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