Hello,
Anyone can suggest me how to make the force field for small cationic system.
Sargol Mazraedoost
Gather Data: Collect data on the molecular system you want to parameterize. This includes information about the molecular structure, bond lengths, bond angles, dihedral angles, partial charges, and other relevant properties. Experimental data can be valuable for validation. Select a Force Field: Choose an appropriate force field. Force fields are sets of parameters that describe the potential energy functions for various types of atoms, bonds, angles, and dihedrals. Common force fields include CHARMM, AMBER, and OPLS, among others. Parameterization:Atomic Charges: Calculate partial atomic charges for each atom in your system. There are various methods for deriving charges, such as quantum chemical calculations (e.g., using programs like Gaussian or DFT calculations) or empirical charge derivation methods (e.g., RESP or ESP charges). Bonded Parameters: Define bond parameters (bond lengths and force constants), angle parameters (equilibrium angles and force constants), and dihedral parameters. These parameters are often determined through quantum calculations or optimization against experimental data. Non-Bonded Parameters: Determine van der Waals (Lennard-Jones) parameters for atom pairs (sigma and epsilon values) and electrostatic interactions (Coulombic interactions). These parameters can be derived from experimental data or quantum calculations. Optimization: Perform optimization calculations to refine the force field parameters. This often involves minimizing the energy of the system with different conformations and comparing the results to experimental data. Validation: Validate your force field by comparing its predictions with experimental or other reliable data. This step helps ensure that your force field accurately represents the behavior of the system. Implementation: Implement your custom force field in a molecular modeling software package. This may require creating or modifying force field files. Simulation: Use your custom force field for molecular dynamics simulations or other types of simulations to study the behavior of the cationic system. Iterate: Force field development is often an iterative process. You may need to refine your parameters based on simulation results and further validation.
Below are the general steps involved:
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Ayaz Anwar
First, optimized the geometry/ structure of the ligand, then calculate the partial charges using, for example, Chimera, then use online server to create parameter for the given small molecule/ligand.
For the online server, you can use ATB, Acpype or swissparam etc. Depending on the force field you are using, you can select any one from these.
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