Scripts that are helpful to setup SWISH simulations. Documentation to be added!
Scripts have been rewritten to rely on ParmEd for better transferabilty and extensibility. Have been tested using Amber type force-fields, with AMBER and GROMACS MD engines, a little bit of OpenMM, too.
- Prepare topologies for water-apolar interface scaling
- Add fragments and adjust inter-ligand repulsion (optional)
- Other useful scripts for analysis (TBA)
N.B. Consider all scripts under development. Please, inform of any issues. Thank you!
Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations
Vladimiras Oleinikovas, Giorgio Saladino, Benjamin P. Cossins, and Francesco L. Gervasio
Journal of the American Chemical Society 2016 138 (43), 14257-14263
DOI: 10.1021/jacs.6b05425
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