These commands control the reading and writing of topology files. Cpptraj supports the following topology file
formats:
| Format | Keyword | Extension | Notes |
| Amber Topology | amber | .parm7 | Only fully-supported format for write |
| PDB | pdb | .pdb | Read Only |
| Mol2 | mol2 | .mol2 | Read Only |
| CIF | cif | .cif | Read Only |
| Charmm PSF | psf | .psf | Limited Write |
| Gromacs Topology | gromacs | .top | Read Only |
| SDF | sdf | .sdf | Read Only |
| Tinker ARC | arc | .arc | Read Only |
For most commands that require a topology one can be specified via two keywords:
parm [<name>] Select topology corresponding to given file name, tag, or name.
parmindex [<#>] Select topology by order in which it was loaded, starting from 0.
The following topology related commands are available:
| Command | Description |
| angleinfo, angles, printangles | Print angle info for selected atoms. |
| atominfo, atoms, printatoms | Print details for selected atoms. |
| bondinfo, bonds, printbonds | Print bond info for selected atoms. |
| bondparminfo | Print the bond parameter table. |
| change | Change specified parts of a topology. |
| charge | Print total charge for selected atoms. |
| comparetop | Compare two topologies and report differences. |
| dihedralinfo, dihedrals, printdihedrals | Print dihedral info for selected atoms. |
| hmassrepartition | Perform hydrogen mass repartitioning. |
| improperinfo, impropers, printimpropers | Print improper info for selected atoms. |
| mass | Print total mass for selected atoms. |
| molinfo | Print molecule info for selected atoms. |
| parm | Load a topology file. |
| parmbox | Modify box info for a loaded topology. |
| parminfo | Print details for selected topology. |
| parmstrip | Remove selected atoms from topology. |
| parmwrite | Write selected topology to file. |
| printub, ubinfo | Print Urey-Bradley info for selected atoms. |
| resinfo | Print residue info for selected atoms. |
| scaledihedralk | Scale selected dihedral force constants. |
| solvent | Change which molecules are considered solvent. |
| updateparameters | Update/add parameters in/to a topology. |