How to Add Parameters for New Atom Types in Autodock
How to Add Parameters for New Atom Types in Autodock
Autodock is a popular software for molecular docking and virtual screening. It uses a force field to describe the interactions between the ligand and the receptor. Sometimes, you may encounter a ligand that contains atom types that are not defined in the default force field. In that case, you need to add parameters for those new atom types before you can run Autodock.
Here are the steps to add parameters for new atom types in Autodock:
Autodock Add Parameters For It To The Parameter Library First
Identify the new atom types and their properties, such as atomic number, mass, charge, covalent radius, and solvation parameter.
Create a modified parameter file that includes the definitions of the new atom types. You can use the default parameter file (AD4_parameters.dat) as a template and append the new definitions at the end of the file. The format of each line is:
atom_type atomic_number mass charge radius solpar
In the parameter files for AutoGrid and AutoDock (*.gpf and *.dpf files), add this command at the top of the file:
parameter_file <modified parameter file name>
Run AutoGrid and AutoDock as usual, using the modified parameter files.
For more details and examples, please refer to this page.Here are some tips and tricks to make your parameter addition process easier and more accurate:
Use a molecular editor or viewer to check the atom types and charges of your ligand. Some common tools are PyMOL, Chimera, Avogadro, and Open Babel.
Use a periodic table or a chemistry reference to look up the atomic number, mass, and covalent radius of the new atom types. You can also use online databases such as PubChem or ChemSpider.
Use empirical formulas or experimental data to estimate the solvation parameter of the new atom types. The solvation parameter is a measure of how much an atom prefers to be in water or in air. A positive value means the atom is hydrophilic (water-loving), while a negative value means the atom is hydrophobic (water-hating). You can also use the values of similar atom types as a guide.
Test your modified parameter file by running a small docking experiment with your ligand and a simple receptor. Compare the results with the default parameter file and see if there are any significant differences in the binding modes or energies.
If you encounter any errors or warnings during the parameter addition or docking process, check the Autodock website or forum for troubleshooting tips and solutions.
By following these steps, you can successfully add parameters for new atom types in Autodock and expand your docking capabilities.In conclusion, adding parameters for new atom types in Autodock is a necessary and useful skill for molecular docking and virtual screening. It allows you to handle ligands that contain uncommon or novel atom types and explore their interactions with receptors. By following the steps and tips outlined in this article, you can easily and accurately add parameters for new atom types in Autodock and enhance your docking results. 0efd9a6b88
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