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Navigation: Documentation / Commands / topcrd2crd


topcrd2crd: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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:
crd - amber restart file
xyz - xyz file
(Default: crd)
-o, --output FORMAT
specify output format for coordinates:
crd - amber restart file
pdb - PDB file
pqr - PDB file with atomic radii and charges
xyz - xyz file
xyzr - xyz file with atomic radii
com - gaussian input file
rbox - rbox format for qhull
traj - amber trajectory file
adf - plain ADF input
adffrag - plain ADF input with one fragment
adf3drism - 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.
-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.
-t, --mangle FORMAT
specify atom names mangling scheme:
none - no translation (1234)
pdb - pdb scheme (4123), keep amber names
charmm - 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


Navigation: Documentation / Commands / topcrd2crd


topcrd2crd: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

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:
crd - amber restart file
xyz - xyz file
(Default: crd)
-o, --output FORMAT
specify output format for coordinates:
crd - amber restart file
pdb - PDB file
pqr - PDB file with atomic radii and charges
xyz - xyz file
xyzr - xyz file with atomic radii
com - gaussian input file
rbox - rbox format for qhull
traj - amber trajectory file
adf - plain ADF input
adffrag - plain ADF input with one fragment
adf3drism - 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.
-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.
-t, --mangle FORMAT
specify atom names mangling scheme:
none - no translation (1234)
pdb - pdb scheme (4123), keep amber names
charmm - 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


Navigation: Documentation / Commands / topcut


topcut: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

topcut

Synopsis

topcut [OPTIONS] [--] OLD MASK NEW

Description

Cut AMBER topology and saves it as new one. Artifical topologies with open valences could be save too but use them only for visualisation purposes not for energy evaluation.

Arguments

OLD
old topology name. If - is provided then topology is read from standard input stream.
MASK
mask specification
NEW
new topology name. If - is provided then topology is written to standard output stream.

Options

-c, --coords CRD
optional coordinates in AMBER coordinate format, coordinates are mandatory for masks containing distance operators (: @)
-f, --maskfile
read mask specification from the first line of the file of name MASK. This option is suitable for the specification of very long masks.
--copybox
copy old box information to new topology
--ignoreerrors
ignore open valences in newly created topology
--ver6
save new topology in version AMBER 6
-v, --verbose
increase output verbosity
--version
output version information and exit
-h, --help
display this help and exit