Duvida System with membrane

[Alana Lígia]

I want to calculate the free energy of the system I'm working on, but I'm unsure whether to use the membrane protein configurations or the solvent calculation configurations. The system consists of two interacting proteins, one of which is anchored to the membrane, but the interaction occurs outside of it, near the top layer. Could you help me with this?

[mariosergi...@gmail.com]

You can probably ignore the membrane (parameter configuration) if the interaction occurs far from it.

[Alana Lígia]

I really appreciate your answer, another question, my system was built with the Charmm force field, but on the website there is only a configuration file for protein-ligand, which is not the case, what do you suggest? Use the available protein-protein one or make some adaptation to the protein-ligand one?

[mariosergi...@gmail.com]

You can use this example as a base https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_membrane_CHARMMff/
Please, don't use the example literally, since it is configured for demonstration purposes