Develop a charge distribution and automatically generate input force field parameters for most organic molecules.

The Antechamber suite automates the process of developing a charge distribution and assigning atom types, and partially automates the process of developing parameters for the various combinations of atom types found in a given molecule. Antechamber can automatically generate input force field parameters for most organic molecules, thereby allowing users to use AMBER, also through the AMPS-NMR web portal, to refine the structure of protein-ligand adducts.

To run this tutorial, download the data attached at bottom of this page.

To perform an Antechamber calculation we must to choose the type of coordinate file we want to upload. In this example we will use have a .pdb file. After selecting the type, upload the molecule file (nngh.pdb) and optionally set the charge of entire molecule or rename it. The latter optional steps can be done in any moment of the calculation setup. In the following picture you can see the welcome page of the Antechamber portal and take an overview of all inputs necessary to load an organic molecule.

When you press the "Load residue" button, the section of "Internal coordinates" will appear. In the left part of your browser there will be a window representing a 3D view of your molecule (see picture below).

In the Internal coordinates section we can see the columns representing the group of atoms (A1, A2, A3, A4), their bond distance (A1-A2), angle value (A1-A2-A3), dihedral angle value (A1-A2-A3-A4) and finally the charge of A1. The button in the red circle will show the value of the corresponding column in the 3D window. It is possible to change any value in the table; by simply pressing the Enter key (or Update button at bottom of page) both the data and the 3D visualization will be updated.

Finally, you can press the "Download ZIP" button in the "Create Parameters and retrieve ff" section to download the compressed archive containing the files created (see the picture below).

This latter picture shows the generated output files, where the inputs for AMPS-NMR web portal are molwe2.pdb, mol.prepi (topology file), mol.frcmod (parameters file). The remaining files are, respectively, the inputs for XPLOR-NIH and CHARMM software.