Topcrd2crd: Difference between revisions

<span style="margin-left: 15px;">topcrd2crd</span>

<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>

<p style="text-indent: 1em; text-align: justify;">Converts AMBER topology and coordinates to coordinates in other format.</p>

{| style="margin-left: 2em; width: 95%;"

| <span style="color: purple;">PARM</span><br/><div style="margin-left: 30px;">topology file name</div>

| <span style="color: purple;">CRD</span><br/><div style="margin-left: 30px;">input coordinates file name or - for standard input</div>

| <span style="color: purple;">OUT</span><br/><div style="margin-left: 30px;">output coordinates file name or - for standard output</div>

|<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;">-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;">-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;">-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;">-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;">--rscale</span><br/><div style="margin-left: 30px;">scale factor for atomic radii (r_new = r * scale + offset)</div>

|<span style="color: blue;">--roffset</span><br/><div style="margin-left: 30px;">offset for atomic radii (r_new = r * scale + offset)</div>

|<span style="color: blue;">-r, --reindex</span><br/><div style="margin-left: 30px;">reindex atom and residue numbers counting from 1</div>

|<span style="color: blue;">--copybox</span><br/><div style="margin-left: 30px;">copy box information to output file</div>

|<span style="color: blue;">--novelocities</span><br/><div style="margin-left: 30px;">do not transfer velocities</div>

|<span style="color: blue;">--nochains</span><br/><div style="margin-left: 30px;">do not print chain IDs into pdb files</div>

|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>

|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>

|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>