posted on 2024-12-30, 04:41authored byDaniel MobergDaniel Moberg, Alec F. White, Justin Provazza, David A. Pearlman
Datasets containing structures, DFT energies and forces, and atomic numbers for two types of systems:
cyclic peptides (69 structures, 963 total conformations)
noncanonical residues with ACE/NME caps (16 structures, 990 total conformations)
Initial cyclic peptide structures were selected from the CREMP dataset. Initial noncanonical residue structures were obtained from the RCSB Protein Data Bank, then capped with ACE/NME residues. Each structure was solvated (water and hexane for cyclic peptides, water for noncanonical monomers) before running a 10 ps NVT molecular dynamics simulation at 500 K. From these trajectories, conformations were selected for running DFT calculations with Psi4. The Psi4 template provided by the SPICE dataset was used to ensure compatibility between datasets and usage with SPICE.