MemTorMD

Forms diverse lipid torroids! MemTorMD allows you to insert proteins into torroidal division pores, as well as in a periplasmic environment context of various heights. Choose the protein, the pore and the area per lipid. The programme will do the rest. Visualise your initial insertion here.

Pores may be formed of either E.coli (inner membrane) or B. subtilis membranes, however the lipid levels are modifiable within the script for custom species.

If you dont need to insert proteins and only want to study pores or other 3D architectures of membranes - use TS2CG GUI https://colab.research.google.com/drive/1Krjt9W5FlHZMGptuhVYpM9W7XRZC023e?usp=sharing A simpler version of MemTorMD we made for general use with other topologies such as vesicles

For more control and for work specifically on toroid lipids use ToroidMaker-basic MemTorMD is heavily dependent on TS2CG a system which allows for pointilism of 3D structures and insertion of lipids along these structures. It adds to this base code, by overlaying a pipeline made of new scripts that can count molecules created in TS2CG, boxing and morphing of custom 3D shapes in this case a pore, aswell as providing a protein insertion method by which simulations can be directly run. Using this method, reproducible pores of different sizes and multilayer lipid systems can be simulated with your protein(s) of interest or investigated for other properties. You may also view your output pore in browser. Inspired by MemProtMD

Use the MemTorMD .pynb attached - an active link is available here: https://colab.research.google.com/drive/1gkD6BOgN_fv5kZ4aQ_q4QbN7JYyT3vlK?usp=sharing