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 |
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 | Limited Write |
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 |
charge | Print total charge for selected atoms. |
comparetop | Compare two topologies and report differences. |
dihedralinfo, dihedrals, printdihedrals | Print dihedral 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. |
resinfo | Print residue info for selected atoms. |
scaledihedralk | Scale selected dihedral force constants |
solvent | Change which molecules are considered solvent |