Experimental variation in solved structures is observed. Molecular dynamics can be used to standardize a 3D database via minimization.
New van der Waals radii parameters for atoms in the GAFF2 ligand forcefield was developed. For proteins and ions, new van der Waals radii parameters were incorporated into the AMBER12sb for proteins.
Bonded (bond types, angle types, improper and proper dihedrals) and non-bonded (mass, charge, sigma, epsilon) parameters for modified amino acids, co-factors and other important ligands were developed and incorporated into the ABMBER12sb forcefield.
Metal ion parametrization was incorporated to stabilize ion-protein-ligand interactions. Bond lengths and bond angles for ion-protein interactions are calculated for each protein.
Modified amino acids: 2MR, ABA, AIB, ALY,CAF, CAS, CCS, SME, CMH, CSS, CYF, FME, IAS, KCX, LLP, M3L, MIS, MLY, NEP, OCS, OCY, OTY, PCA, PHD, PPN, PTR, SBG, SCH, SEP, SGB, TPO, TPQ, TRQ.
Co-factors and other ligands: 1W9, 6FA, A3P, QCP, ADP, AGS, AMP, ANP, APC, AR6, ATP, ATR, B12, BCL, BVQ, CLA, COA, COH, DAT, DTP, FA8, FAD, FDA, FMN, FNR, FPP, GAR, GDP, GMP, GNP, GSH, GTP, H4B, HEC, HEM, IMP, MGD, MGP, NAD, NAI, NAP, NCN, NDP, NHW, P3S, PLG, PLP, PLS, RBF, SAH, SAM, SFG, TYD, UDP, UMP, XMP.