Step 4 - Results
Now that the wizard has completed you’ll see that the process has yielded a species with a full forcefield assignment, ready to do your simulated bidding. That was easy, wasn’t it?
Some things to consider / think about when using this approach:
- Many simulators (including myself) have a lot of faith in the underlying parameter set (OPLS-AA) used by LigParGen, so it should give usable results for a great many molecules. However, you may find systems that do not work, so don’t treat it as a guarantee.
- Charges are assigned to species atoms, not atom types, so you may need to ensure that this particular source of charges is selected / forced in the
Forcefield
. - If you use LigParGen, please cite it as it’s a fantastic resource. The necessary references are produced below for convenience.
References:
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“Potential energy functions for atomic-level simulations of water and organic and biomolecular systems.”, W. L. Jorgensen and J. Tirado-Rives, Proc. Nat. Acad. Sci. USA 102, 6665-6670 (2005).
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“1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations.”, L. S. Dodda, J. Z. Vilseck, J. Tirado-Rives, and W. L. Jorgensen, Phys. Chem. B 121 (15), 3864-3870 (2017).
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“LigParGen web server: An automatic OPLS-AA parameter generator for organic ligands.”, L. S. Dodda, I. Cabeza de Vaca, J. Tirado-Rives, and W. L. Jorgensen, Nucleic Acids Research 45 (W1), W331-W336 (2017).