Molecular dynamic simulation of protein- ligand complex. How do I set up a molecular dynamic simulation for...

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Biology

Molecular dynamic simulation of protein- ligandcomplex.
How do I set up a molecular dynamic simulation for a protein-ligand complex with a cobalt in the 2++ state? In other words, arethere topology and parameter files that contain parameter forcobalt ion which are compatible with NAMD?

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If you have got the correct pose from docking result and you have a target in your hand then you start MD simulation So for MD is concerned using NAMD You cant directly run simulation because See Answer

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Molecular dynamic simulation of protein- ligand complex. How do I set up a molecular dynamic simulation for...

70.2K

Verified Solution

Question

Biology

Molecular dynamic simulation of protein- ligandcomplex.
How do I set up a molecular dynamic simulation for a protein-ligand complex with a cobalt in the 2++ state? In other words, arethere topology and parameter files that contain parameter forcobalt ion which are compatible with NAMD?

Answer & Explanation Solved by verified expert

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Molecular dynamic simulation of protein- ligand complex. How do I set up a molecular dynamic simulation for...

70.2K

Verified Solution

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Biology

Molecular dynamic simulation of protein- ligandcomplex.How do I set up a molecular dynamic simulation for a protein-ligand complex with a cobalt in the 2++ state? In other words, arethere topology and parameter files that contain parameter forcobalt ion which are compatible with NAMD?

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Molecular dynamic simulation of protein- ligandcomplex.
How do I set up a molecular dynamic simulation for a protein-ligand complex with a cobalt in the 2++ state? In other words, arethere topology and parameter files that contain parameter forcobalt ion which are compatible with NAMD?