Sentence examples for general amber force from inspiring English sources
After preprocessing, the optimized structure of and atomic charges for the ligand are obtained according to the AM1-BCC method [34] and the topology of the ligand is generated according to the General Amber Force Field (GAFF) [35].
Ligands were described with the general Amber force field GAFF [52].
Atom types in the non standard residues were adapted from the general AMBER force field.
Standard Amber ff99 force field was assigned to the protein, and the general AMBER force field (gaff) was assigned to the ligands including the co-factor InsP6 [35] [37].
The Amber99 force field parameters were used for all protein residues [89] and ligand parameters were assigned with the general AMBER force field (GAFF) and the corresponding RESP charges using the Antechamber module of AMBER.
The energy of the solvated molecular complex was minimised using the general AMBER force field with a steepest descent method that was continued for 50,000 time steps (one time step one femtosecond) or until the RMSD had fallen below 0.01 Å between successive time steps.
Multiple molecular dynamics simulations (MMDSs) were performed using the PMEMD module of the AMBER 8.0 program [50] with a revised force field (to be published) that is based on the second-generation AMBER force field (frcmod.ff99SB) [51].ff99SB
This energy is calculated according to Equations 1 and 2 using the second-generation AMBER force field [18].
MD simulations were implemented in AMBER [ 40], using an all-atom force field based on the generalized AMBER force field (GAFF) [ 41] for [C2mim] cation [ 42], the standard Cl- anion force field for chloride ions, and the carbohydrate force field, GLYCAM [ 43], for glucose.
Unlike the other AMBER force fields studied, the AMBER-99SB potential shows very large divergence toward greater polar and, much more notably, non-polar surface areas.
This energy is calculated according to Equations 1 and 2 using the second generation AMBER force field [29].
