| Introduction |
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VAD-MM/GBSA is a webserver for protein-ligand (the ligand must be a small molecule compound) binding free energy prediction by using the variable atomic dielectric MM/GBSA method. In VAD-MM/GBSA, simuled annealing and XGBoost regression are used for dielectric optimization.
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Please carefully read the Help page and check your input files before submitting your job.
Note that (1) the topology (.prmtop format) and trajectory (.nc format) files must be generated by AMBER package; (2) if GROMACS (or NAMD, etc.) was used for conformation sampling, please first convert the input files to AMBER format; (3) spaces are not allowed in uploaded filenames; (4) make sure waters and ions excluded in the uploaded files; (5) the native complex structure is optional.
An email with results will be sent to you once your job is completed successfully.
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There is an example for using the VAD-MM/GBSA webserver below.
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