Hi!
I want to use “biobb_amber_CpHMD_notebook”, to prepare my system which is an ion channel for running CpHMD with Amber.
My questions are:
Is it possible to embed the protein in membrane with biobb in some step? or use the already prepared membrane embedded solvated system from CHARMM-GUI as an input? If so, to prepare the initial parameters and topology, which terms should be added to include the forcefields of ions and lipids to be taken into consideration. or what are the required changes in the steps.
I’m afraid there’s no module in the BioBB library at this time to embed the protein in membrane.
Using the CHARMM-GUI to prepare the system and use the results as an input for the notebook should be possible, although you will need to modify the workflow. Sorry I am not familiar with the outputs of the server, so I can not tell you what exactly needs to be modified. About the force fields, it should be enough to add them to all the leap building blocks (leap_gen_top, leap_solvate, leap_add_ions), using the force_field property and/or the input parameters input_params_path and input_source_path.
If you try it and find problems, please contact us again and we will try to help you during the process.