03. Membrane Builder скачать в хорошем качестве

03. Membrane Builder

Here is the Membrane Builder tutorial. Join MolCube apps to expand your research horizons! Try it : https://apps.molcube.com/ For more information : https://apps.molcube.com/help/getting... Script : Membrane Builder is a module for defining membrane systems for molecular dynamics with or without solutes. In the left sidebar, go to ‘MolCube-Builder’ and select ‘Membrane Builder’. In this demo, we start with the 7Y9B protein already loaded via PDB Reader. First, type your project title—“7Y9B M‑Protein Bilayer,” for example. Under Membrane Type, select Bilayer, since we’re embedding a membrane protein, and set Box Shape to Rectangular for an orthogonal box. We’ll select the commonly used CHARMM‑FF force field—please ensure it matches exactly the force field you specified in PDB Reader. If you only need the membrane, enable Membrane Only—perfect for pure lipid setups like LNP formulation or lipid biophysics studies—and follow the same sequence of steps. In Search for Project, type “7Y9B,” pick the PDB Reader entry, and click Submit. Then click Next. The second step is alignment. Here you choose how to orient your protein within the membrane. The options—As‑Is, Principal Axis, and PPM—allow you to translate or rotate the structure so its transmembrane region aligns correctly with the bilayer. For realistic embedding we recommend PPM, which follows the OPM database standard. Once selected, click Next. In Step 3, you define the lipid composition. You may enter individual lipid species and their mole fractions manually or pick from a Predefined Bio‑Membrane template. In this demo we’ll choose the “PMM” template, then click Apply so that the lipid types and ratios are populated automatically. After reviewing the composition for accuracy, click Submit and advance to the next stage. The fifth step lets you configure your simulation box and environment. Here, you can specify water thickness above and below the bilayer, set the hydration number, that is, waters per lipid, choose whether to neutralize only, or add a specific ion concentration, and define your simulation temperature in Kelvin. You can also enable Hydrogen Mass Repartitioning for a four-fs time step, and select your MD engine, for example, GROMACS. Membrane Builder will then generate all necessary input files for the chosen engine. Click “Next” when you’re ready. Finally, in Step 6 you perform a full review. The interface displays a complete 3D Visualization alongside System Info, detailing component ratios, atom counts, net charge, and an energy breakdown. If everything looks correct, click Download to retrieve PDB, GRO, TOP, XML—or grab the entire project bundle. From there you can run your simulation files directly on your local workstation or server, or import the project into Molcube‑Simulator for one‑click energy minimization, equilibration, and production runs, all the way through to analysis. That completes the workflow to embed 7Y9B in a PMm bilayer using Membrane Builder. Enjoy your simulations!