If a window appeared saying that “ The product will run in Evaluation Mode” then click OK. You can SAVE the ligand with correct protonation state in your desired file format. Adjust the protonation state of the ligand:Ĭlick on MS and then Calculations > Protonation> Major Microscopes> a window will appear where you can input your desired pH and click OK and it should show a new window with the correct protonation state of the ligand at your desired pH. MS supports SDF, MOL, MOL2, PDB and all other common file formats.ġ.2. You can download the package from ĭraw the ligand in MS or import the SMILE or InchI Keys or open an supplied ligand. MarvinSketch is an amazing JAVA based functionality which includes several basic and advanced functionalities and completely free for academic use. Molecular Docking: Tutorial Docking with Autodock Vina: A step by step guide for Beginners or Advanced Users
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