It is necessary to sample relevant conformations of each amino-acid residue to generate transferable parameters. In previous works by some of us, conformational sampling was obtained through classical MD simulations. Here, we employ a more focused strategy instead, using the smoothed backbone-dependent rotamer library of Shapovalov and Dunbrack. This library contains, for each amino acid, conditional probabilities of finding a specific combination of backbone and side-chain dihedral angles based on entries from the Protein Data Bank (PDB). We include rotamers for each amino acid in order of the most commonly occurring. The total number of possible rotamers is rather large. Therefore, for each amino acid, we only included rotamers (based on backbone/side-chain dihedral angles combinations) until the cumulative fraction of covered structures from the database reached 80%. For glycine and alanine, which do not have any side-chain rotamers, the backbone dihedrals from valine were used. For cysteine, lysine, aspartate, glutamate, and histidine, alternative side-chain protonation states were also included, using the same dihedral angles as the parent amino acid. Specifically, we included the disulfide-bonded cysteine (CYX), deprotonated cysteine (CYD) and lysine (LYD), and the protonated aspartate (ASH) and glutamate (GLH), along with the δ (HID) and (HIE) protonated variants of neutral histidine. Initial geometries of the amino acids were constructed with the dihedral angles as an input using the FragBuilder tool. The main set of parameters used the acetyl and N-methyl capping groups, in order to mimic the environment of a typical protein backbone (Fig. ).