Umbrella Sampling for Protein-Ligand Complexes

User discussions
1

I would like to perform umbrella sampling for protein-ligand complexes. The ligand is a small organic compound, i.e. cryptamygin-A. Which is the best force field to use? Are there any helpful articles, reviews, papers or tutorials for such projects?

Thanks in advance

2

The “best” force field is the one for which you can easily and accurately parametrize the ligand.

Articles abound for these kinds of calculations. The umbrella sampling tutorial I wrote (Umbrella Sampling) can easily be adapted for your case, you just don’t pull along a single Cartesian axis, you define a sensible reaction coordinate between the ligand and its binding site and the bias should likely be applied in all three dimensions.

3

Thank you for the quick response