Can slipids be used instead of Berger lipid parameters in the Membrane Protein: KALP15 in DPPC tutorial? I am looking for an alternative to CHARMM-GUI.
In general you can parametrize however you want a system, as long as the parameters are consistent (e.g. if you use CHARMM36m for the protein you should also use it for the lipids and use the corresponding TIP3p and CGenFF for small molecules etc…, so DO NOT mix force fields). Which force field to chose is a question then of what quantities of the system you are trying to model, and that will require some literature search. Being this a tutorial I would say that it is irrelevant if you go for slipids and the corresponding AMBER force field, although this might require some small changes in the tutorial steps (e.g. the naming in the deuterium order parameters).
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Thank you. Do you mean relevant instead of irrelevant? Or you mean it’s irrelevant to use slipids and the corresponding AMBER force field in this tutorial? Sorry for the confusion.
Sorry I didn’t express myself clearly, I mean that this is a tutorial aimed at learning some basics of lipid bilayer simulations and analysis. As such, since you do not care about the results being scientifically sound, you can pick whatever force field you want and go with it (but still try to be consistent, i.e., don’t mix them). For example, the Berger united-atom model proposed in the tutorial is outdated and probably it would be better not to use them anymore (as the author of the tutorial states), but even if you use them the general point of the tutorial is still valid, i.e., learn some basics. Nowadays I would say that the was majority of people would prepare a system like this - protein embedded in a lipid bilayer - with CHARMM-GUI.
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