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{{DISPLAYTITLE:topcrd2crd}} | |||
Navigation: [[Documentation]] / [[Commands]] / [[topcrd2crd]] | |||
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<div style="text-align: center">topcrd2crd: version 2.231.418d045(2020-03-01 18:49) [CATs - Conversion And Analysis Tools]</div>'''Name''' | |||
<span style="margin-left: 15px;">topcrd2crd</span> | |||
'''Synopsis''' | |||
<span style="color: maroon; margin-left: 15px;">topcrd2crd</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">PARM</span> <span style="color: purple;">CRD</span> <span style="color: purple;">OUT</span> | |||
'''Description''' | |||
<p style="text-indent: 1em; text-align: justify;">Converts AMBER topology and coordinates to coordinates in other format.</p> | |||
'''Arguments''' | |||
{| style="margin-left: 2em; width: 95%;" | |||
|- style="vertical-align: top; background-color: #e6e6e6;" | |||
| <span style="color: purple;">PARM</span><br/><div style="margin-left: 30px;">topology file name</div> | |||
|- style="vertical-align: top;" | |||
| <span style="color: purple;">CRD</span><br/><div style="margin-left: 30px;">input coordinates file name or - for standard input</div> | |||
|- style="vertical-align: top; background-color: #e6e6e6;" | |||
| <span style="color: purple;">OUT</span><br/><div style="margin-left: 30px;">output coordinates file name or - for standard output</div> | |||
|} | |||
'''Options''' | |||
{| style="margin-left: 2em; width: 95%;" | |||
|- style="vertical-align: top; background-color: #e6e6e6;" | |||
|<span style="color: blue;">-i, --input FORMAT</span><br/><div style="margin-left: 30px;">specify input format for coordinates:<br /><span></span> <span style="color: green;">crd</span> - amber restart file<br /><span></span> <span style="color: green;">xyz</span> - xyz file</div><span style="color:purple; margin-left: 30px;">(Default: crd)</span> | |||
|- style="vertical-align: top;" | |||
|<span style="color: blue;">-o, --output FORMAT</span><br/><div style="margin-left: 30px;">specify output format for coordinates:<br /><span></span> <span style="color: green;">crd</span> - amber restart file (ASCII)<br /><span></span> <span style="color: green;">bcrd</span> - amber restart file (NetCDF)<br /><span></span> <span style="color: green;">pdb</span> - PDB file<br /><span></span> <span style="color: green;">pqr</span> - PDB file with atomic radii and charges<br /><span></span> <span style="color: green;">xyz</span> - xyz file<br /><span></span> <span style="color: green;">xyzr</span> - xyz file with atomic radii<br /><span></span> <span style="color: green;">com</span> - gaussian input file<br /><span></span> <span style="color: green;">orca</span> - orca input file<br /><span></span> <span style="color: green;">pc</span> - point charges file<br /><span></span> <span style="color: green;">rbox</span> - rbox format for qhull<br /><span></span> <span style="color: green;">traj</span> - amber trajectory file<br /><span></span> <span style="color: green;">adf</span> - plain ADF input<br /><span></span> <span style="color: green;">adffrag</span> - plain ADF input with one fragment<br /><span></span> <span style="color: green;">adf3drism</span> - plain ADF input for 3D-RISM</div><span style="color:purple; margin-left: 30px;">(Default: pdb)</span> | |||
|- style="vertical-align: top; background-color: #e6e6e6;" | |||
|<span style="color: blue;">-m, --mask MASK</span><br/><div style="margin-left: 30px;">only atoms selected according to MASK will be converted otherwise all atoms are used. Mutually exclusive with 'maskfile' option.</div> | |||
|- style="vertical-align: top;" | |||
|<span style="color: blue;">-f, --maskfile MASKFILE</span><br/><div style="margin-left: 30px;">only atoms selected according to the mask will be converted otherwise all atoms are used. 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.</div> | |||
|- style="vertical-align: top; background-color: #e6e6e6;" | |||
|<span style="color: blue;">--chrgmask MASK</span><br/><div style="margin-left: 30px;">only atoms selected according to MASK will be included as point charges. Mutually exclusive with 'chrgmaskfile' option.</div> | |||
|- style="vertical-align: top;" | |||
|<span style="color: blue;">--chrgmaskfile MASKFILE</span><br/><div style="margin-left: 30px;">only atoms selected according to the mask will be included as point charges. 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 'chrgmask' option.</div> | |||
|- style="vertical-align: top; background-color: #e6e6e6;" | |||
|<span style="color: blue;">-t, --mangle FORMAT</span><br/><div style="margin-left: 30px;">specify atom names mangling scheme:<br /><span></span> <span style="color: green;">none</span> - no translation (1234)<br /><span></span> <span style="color: green;">pdb</span> - pdb scheme (4123), keep amber names<br /><span></span> <span style="color: green;">charmm</span> - charmm name scheme (1234), mangle parm99 names</div><span style="color:purple; margin-left: 30px;">(Default: pdb)</span> | |||
|- style="vertical-align: top;" | |||
|<span style="color: blue;">--rscale</span><br/><div style="margin-left: 30px;">scale factor for atomic radii (r_new = r * scale + offset)</div> | |||
|- style="vertical-align: top; background-color: #e6e6e6;" | |||
|<span style="color: blue;">--roffset</span><br/><div style="margin-left: 30px;">offset for atomic radii (r_new = r * scale + offset)</div> | |||
|- style="vertical-align: top;" | |||
|<span style="color: blue;">-r, --reindex</span><br/><div style="margin-left: 30px;">reindex atom and residue numbers counting from 1</div> | |||
|- style="vertical-align: top; background-color: #e6e6e6;" | |||
|<span style="color: blue;">--copybox</span><br/><div style="margin-left: 30px;">copy box information to output file</div> | |||
|- style="vertical-align: top;" | |||
|<span style="color: blue;">--novelocities</span><br/><div style="margin-left: 30px;">do not transfer velocities</div> | |||
|- style="vertical-align: top; background-color: #e6e6e6;" | |||
|<span style="color: blue;">--nochains</span><br/><div style="margin-left: 30px;">do not print chain IDs into pdb files</div> | |||
|- style="vertical-align: top;" | |||
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div> | |||
|- style="vertical-align: top; background-color: #e6e6e6;" | |||
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div> | |||
|- style="vertical-align: top;" | |||
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div> | |||
|} | |||
Latest revision as of 22:32, 3 March 2020
Navigation: Documentation / Commands / topcrd2crd
topcrd2crd: version 2.231.418d045(2020-03-01 18:49) [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 (ASCII) bcrd - amber restart file (NetCDF) pdb - PDB file pqr - PDB file with atomic radii and charges xyz - xyz file xyzr - xyz file with atomic radii com - gaussian input file orca - orca input file pc - point charges 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 otherwise all atoms are used. Mutually exclusive with 'maskfile' option.
|
| -f, --maskfile MASKFILE only atoms selected according to the mask will be converted otherwise all atoms are used. 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.
|
| --chrgmask MASK only atoms selected according to MASK will be included as point charges. Mutually exclusive with 'chrgmaskfile' option.
|
| --chrgmaskfile MASKFILE only atoms selected according to the mask will be included as point charges. 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 'chrgmask' 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
|