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Revision as of 22:33, 3 July 2018
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
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CRD input coordinates file name or - for standard input
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OUT output coordinates file name or - for standard output
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Options
-i, --input FORMAT specify input format for coordinates: (Default: crd)
crd - amber restart file xyz - xyz file |
-o, --output FORMAT specify output format for coordinates: (Default: pdb)
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 |
-m, --mask MASK only atoms selected according to MASK will be converted. Mutually exclusive with 'maskfile' option.
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-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.
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-t, --mangle FORMAT specify atom names mangling scheme: (Default: pdb)
none - no translation (1234) pdb - pdb scheme (4123), keep amber names charmm - charmm name scheme (1234), mangle parm99 names |
--rscale scale factor for atomic radii (r_new = r * scale + offset)
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--roffset offset for atomic radii (r_new = r * scale + offset)
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-r, --reindex reindex atom and residue numbers counting from 1
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--copybox copy box information to output file
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--novelocities do not transfer velocities
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--nochains do not print chain IDs into pdb files
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-v, --verbose increase output verbosity
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--version output version information and exit
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-h, --help display this help and exit
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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: (Default: crd)
crd - amber restart file xyz - xyz file |
-o, --output FORMAT specify output format for coordinates: (Default: pdb)
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 |
-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: (Default: pdb)
none - no translation (1234) pdb - pdb scheme (4123), keep amber names charmm - charmm name scheme (1234), mangle parm99 names |
--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.
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MASK mask specification
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NEW new topology name. If - is provided then topology is written to standard output stream.
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Options
-c, --coords CRD optional coordinates in AMBER coordinate format, coordinates are mandatory for masks containing distance operators (: @)
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-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.
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--copybox copy old box information to new topology
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--ignoreerrors ignore open valences in newly created topology
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--ver6 save new topology in version AMBER 6
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-v, --verbose increase output verbosity
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--version output version information and exit
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-h, --help display this help and exit
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