Hello everyone, I am using Gromacs 2024.2 version of MD simulations and my question is
"When performing MD simulations on a protein-ligand complex involving a cofactor and a substrate, is it necessary to include the cofactor in each simulation for different substrates? How can I effectively isolate and analyze the protein dynamics in a complex with only one ligand (substrate), excluding the cofactor from the resulting trajectories?"
Kindly clarify my question, your help is greatly appreciated.
Thank you
"is it necessary to include the cofactor in each simulation for different substrates?", it depends on your reserach goal, however, generally, it is receommended if that cofactor is necessary for the function/action, it should be there.
"How can I effectively isolate and analyze the protein dynamics in a complex with only one ligand (substrate), excluding the cofactor from the resulting trajectories?" using index groups, you can analyze any part of the system/complex. Make an index of protein and ligand and extract that part of the simulation only. You can make a sub-copy or just run the analysis on those index groups.
To perform MD simulations with two ligands in GROMACS:
All of which can be easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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