Amber ff24EXP-GA, Based on Empirical Ramachandran Distributions of Glycine and Alanine Residues in Water.

ABSTRACT: Molecular dynamics (MD) offers important insights into intrinsically disordered peptides and proteins (IDPs) at a level of detail that often surpasses that available through experiments. Recent studies indicate that MD force fields do not reproduce intrinsic conformational ensembles of amino acid residues in water well, which limits their applicability to IDPs. We report a new MD force field, Amber ff24EXP-GA, derived from Amber ff14SB by optimizing the backbone dihedral potentials for guest glycine and alanine residues in cationic GGG and GAG peptides, respectively, to best match the guest residue-specific spectroscopic data. Amber ff24EXP-GA outperforms Amber ff14SB with respect to conformational ensembles of all 14 guest residues x (G, A, L, V, I, F, Y, D^p, E^p, R,

SUBMITTER: Suresh A 

PROVIDER: S-EPMC11912210 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature