Problem during minimization and molecular docking



  • Dear Sir,
    I have come to know Samson with fantastic features. I am facing some problem using your software. During Molecular Dynamics study, I can’t minimize my prepared protein-ligand complex. It shows some error message in minimization stage.
    I want to dock my protein with ligand libraries, but the problem is I could not load my ligand library. Is there any specific ligand (library) format? I loaded ligand Library in .mol, .mol2, .pdb, .sdf, .pdbqt format. Would you help me to solve these problems?



  • Thank you @Rahad !
    Do you mean the minimization step in the AutoDock Vina Extended module? What error does it show?

    As for ligand libraries, AutoDock Vina Extended module supports libraries with ligands in formats that can be opened in SAMSON, including .pdb, .mol2, .sdf, .xyz, etc, but not .mol and .pdbqt for now. You do not need to import all the ligands in SAMSON, you just need to provide the path to the folder with a ligand library.


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