Topcrd2crd

Name

topcrd2crd

Synopsis

topcrd2crd [OPTIONS] [--] PARM CRD OUT

Description

Converts AMBER topology and coordinates to coordinates in other format.

Arguments

PARM topology file name

CRD input coordinates file name or - for standard input

OUT output coordinates file name or - for standard output

Options

-i, --input FORMAT specify input format for coordinates: <green>crd</green> - amber restart file <green>xyz</green> - xyz file (Default: crd)

-o, --output FORMAT specify output format for coordinates: <green>crd</green> - amber restart file <green>pdb</green> - PDB file <green>pqr</green> - PDB file with atomic radii and charges <green>xyz</green> - xyz file <green>xyzr</green> - xyz file with atomic radii <green>com</green> - gaussian input file <green>rbox</green> - rbox format for qhull <green>traj</green> - amber trajectory file <green>adf</green> - plain ADF input <green>adffrag</green> - plain ADF input with one fragment <green>adf3drism</green> - plain ADF input for 3D-RISM (Default: pdb)

-m, --mask MASK only atoms selected according to MASK will be converted. Mutually exclusive with 'maskfile' option. (Default: )

-f, --maskfile MASKFILE only atoms selected according to the mask will be converted. The mask specification is read from the first line of the file of name MASKFILE. This option is suitable for the specification of very long masks. Mutually exclusive with 'mask' option. (Default: )

-t, --mangle FORMAT specify atom names mangling scheme: <green>none</green> - no translation (1234) <green>pdb</green> - pdb scheme (4123), keep amber names <green>charmm</green> - charmm name scheme (1234), mangle parm99 names (Default: pdb)

--rscale scale factor for atomic radii (r_new = r * scale + offset)

--roffset offset for atomic radii (r_new = r * scale + offset)

-r, --reindex reindex atom and residue numbers counting from 1

--copybox copy box information to output file

--novelocities do not transfer velocities

--nochains do not print chain IDs into pdb files

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit