Materials for five day workshop on using MSLD (including ALF and MSLD_py_prep) for drug discovery and protein engineering
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Most of these scripts will be run using the Slurm Workload Manager.
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We highly encourage you work in a Linux environment, since CUDA is no longer supported using the Apple installation.
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While note explicitly required, please try to have a CHARMM-GUI account, which is free of charge at: charmm-gui.org
https://iu.zoom.us/j/84640919546?pwd=NWp5cFNuNGhNSWphTmJCSWNMbjZXQT09 Meeting ID: 846 4091 9546 Password: msldFE23
| Date | Program |
|---|---|
| Mon, July 31, 2023 | Installing CHARMM, pyCHARMM, and pyALF |
| Tue, August 1, 2023 | Overview of the theories behind free energy methods Overview of theory behind MSLD and ALF Basic steps of writing CHARMM/pyCHARMM scripts |
| Wed, August 2, 2023 | Running ALF Preparing inputs for ALF using msld_py_prep tool. |
| Thu, August 3, 2023 | Using ALF/MSLD to perform ligand perturbation and compute relative free binding energies |
| Fri, August 4, 2023 | Using ALF/MSLD to perform protein perturbation to compute relative folding free energies Using ALF/MSLD to perform constant pH MD simulations |
Zoom video recordings of each day's program will be posted online here: https://iu.mediaspace.kaltura.com/channel/MSLD+Workshop+2023/309046192
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