Topcrd2crd: Difference between revisions
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Navigation: [[Documentation]] / [[Commands]] / [[topcrd2crd]] | Navigation: [[Documentation]] / [[Commands]] / [[topcrd2crd]] | ||
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<div style="text-align: center">topcrd2crd: version 2. | <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> | <span style="margin-left: 15px;">topcrd2crd</span> | ||
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|<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> | |<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;" | |- 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<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;">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> | |<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;" | |- 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. Mutually exclusive with 'maskfile' option.</div> | |<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;" | |- 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. 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> | |<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;" | |- 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> | |<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> | ||