Step 1: Identify the new atom types and their properties
The first step is to identify the new atom types and their properties, such as atomic number, mass, charge, covalent radius, and solvation parameter. You can use online databases or tools to find these information, such as [PubChem], [ChemSpider], or [Open Babel]. For example, if you want to add parameters for selenium (Se), you can find its properties from [PubChem] as follows:
PropertyValue
Atomic number34
Mass78.971 u
Charge0
Covalent radius1.16 A
Solvation parameter-0.00110 kcal/mol/A^3
Step 2: Add the new atom types to the AD4_parameters.dat file
The next step is to add the new atom types to the AD4_parameters.dat file. You can find this file in the folder where you installed Autodock, or you can download it from [here]. You need to open this file with a text editor and append a new line for each new atom type at the end of the file. The format of each line is as follows:
atom_par X Rii epsii vol solpar Rij_hb epsij_hb hbond rec_index map_index bond_index comment
Where:
X is the symbol of the new atom type.
Rii is the sum of van der Waals radii of two like atoms (in Angstrom).
epsii is the van der Waals well depth (in kcal/mol).
vol is the atomic solvation volume (in Angstrom^3).
solpar is the atomic solvation parameter (in kcal/mol/A^3).
Rij_hb is the hydrogen bond radius of the heteroatom in contact with a hydrogen (in Angstrom).
epsij_hb is the well depth of hydrogen bond (in kcal/mol).
hbond is an integer indicating the type of hydrogen bonding atom (0=no H-bond, 1=H-bond donor, 2=H-bond acceptor).
rec_index is initialized to -1, but later on holds the count of how many of this atom type are in receptor.
map_index is initialized to -1, but later on holds the index of the Autogrid map.
bond_index is used in Autodock to detect bonds; see "mdist.h", enum C,N,O,H,XX,P,S.
comment is an optional comment that starts with a sign.
You need to calculate or estimate some of the parameters based on the properties of the new atom types. For example, you can use the following formulas to calculate Rii and vol:
Rii = 2 * covalent radius
vol = (4/3) * pi * (Rii/2)^3
You can also use the values of similar atom types as references to estimate epsii, Rij_hb, epsij_hb, and hbond. For example, you can use the values of sulfur (S) as references for selenium (Se), since they belong to the same group in the periodic table. Alternatively, you can use empirical methods or quantum mechanical calculations to obtain more accurate values of these parameters, but that is beyond the scope of this article.
For example, if you want to add parameters for selenium (Se), you can append the following line to the AD4_parameters.dat file:
atom_par Se 2.32 0.291 65.449 -0.00110 0.0 0.0 0 -1 -1 4 Non H-bonding
Where:
Se is the symbol of selenium.
2.32 is the sum of van der Waals radii of two selenium atoms (2 * 1.16).
0.291 is the van der Waals well depth of selenium, estimated from sulfur (0.250).
65.449 is the atomic solvation volume of selenium, calculated from (4/3) * pi * (2.32/2)^3.
-0.00110 is the atomic solvation parameter of selenium, obtained from [PubChem].
0.0 is the hydrogen bond radius of selenium, assumed to be zero since selenium is not a hydrogen bonding atom.
0.0 is the well depth of hydrogen bond of selenium, assumed to be zero since selenium is not a hydrogen bonding atom.
0 is the integer indicating that selenium is not a hydrogen bonding atom.
-1 is the initial value of rec_index.
-1 is the initial value of map_index.
4 is the bond_index of selenium, corresponding to XX in "mdist.h".
Non H-bonding is an optional comment.
Step 3: Add the parameter_file command to the gpf and dpf files
The final step is to add the parameter_file command to the gpf and dpf files. The gpf file is the grid parameter file that specifies how to generate the grid maps for Autogrid. The dpf file is the docking parameter file that specifies how to perform the docking for Autodock. You need to open these files with a text editor and add the following line at the top of each file:
parameter_file AD4_parameters.dat
This tells Autogrid and Autodock to use the modified AD4_parameters.dat file that contains the new atom types. You need to make sure that this file is in the same folder as the gpf and dpf files, or you need to specify the full path of this file in the parameter_file command.
Conclusion
In this article, we have shown you how to add parameters for new atom types in Autodock step by step. You need to identify the new atom types and their properties, add them to the AD4_parameters.dat file, and add the parameter_file command to the gpf and dpf files. By doing so, you can avoid the error message of unknown receptor type and perform molecular docking and virtual screening with new atom types using Autodock.
We hope this article was helpful for you. If you have any questions or comments, please feel free to contact us or leave a comment below.
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