What is Gaff force field?
We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens.
What is antechamber in Amber?
Antechamber is a set of auxiliary programs for molecular mechanic (MM) studies. As an accessory module in the AmberTools package, antechamber can generate input automatically for most organic molecules in a database. The algorithms behind these manipulations may be useful outside the Amber family of programs as well.
What is the default state of the antechamber?
zero
By default Antechamber will have set the values to zero.
What is CGenFF?
CGenFF is an organic force field explicitly aimed at simulating drug-like molecules in a biological environment represented by the CHARMM additive biomolecular force fields.
What is MMFF94?
The MMFF94 force field (and the related MMFF94s) were developed by Merck and are sometimes called the Merck Molecular Force Field, although MMFF94 is no longer considered an acronym. The method provides good accuracy across a range of organic and drug-like molecules.
What does antechamber word mean?
noun. a chamber or room that serves as a waiting room and entrance to a larger room or an apartment; anteroom.
How do you cite the Amber20?
When citing Amber20 or AmberTools21 please use the following: D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, S.R.
What is AM1 BCC?
Abstract. We present the first global parameterization and validation of a novel charge model, called AM1-BCC, which quickly and efficiently generates high-quality atomic charges for computer simulations of organic molecules in polar media.
What is charmm36?
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them.
What is MOL2?
A MOL2 file contains information about a molecule model saved in the SYBYL MOL2 format. It stores multiple records, such as MOLECULE, ATOM, BOND, SUBSTRUCTURE, and SET, along with 3D coordinates specifying the structure of atoms within a protein or other chemical compound. MOL2 files are similar to . MOL files.
What is Urey Bradley?
The Urey-Bradley component (cross-term accounting for angle bending using 1,3 nonbonded interactions) comprises the fifth term, where is the respective force constant and is the distance between the 1,3 atoms in the harmonic potential. Nonbonded interactions between pairs of atoms are represented by the last two terms.