Explicit values for each atom's mass and partial charge, used by the force field to calculate physical interactions. Connectivity Tables: Bonds: Explicit pairs of atoms that are chemically bonded. Angles: Triplets of atoms forming specific bond angles.
Ensure you also have a corresponding coordinate file ( .pdb or .dcd ). psf.rar
Use a utility like WinRAR or 7-Zip to extract the .psf file from the archive. Explicit values for each atom's mass and partial
Used to maintain planarity (e.g., in aromatic rings). 4. Usage Instructions To utilize the contents of psf.rar , follow these steps: Extraction: Ensure you also have a corresponding coordinate file (
Quartets of atoms defining rotation around bonds.
If your software requires a different topology format (like GROMACS .top ), use tools like vmd or parmed to convert the extracted PSF.
In a NAMD configuration file, point to the extracted file: structure input.psf .