Topcrd2crd: Difference between revisions

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:
crd - amber restart file
xyz - xyz file

(Default: crd)

-o, --output FORMAT

specify output format for coordinates:
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

(Default: pdb)

-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:
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

@@ Line 1: / Line 1: @@
-{{lowercase}}
+{{DISPLAYTITLE:topcrd2crd}}
+Navigation: [[Documentation]] / [[Commands]] / [[topcrd2crd]]
+----
+<div style="text-align: center">topcrd2crd: version 2.231.418d045(2020-03-01 18:49) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-'''Name'''
+<span style="margin-left: 15px;">topcrd2crd</span>
-topcrd2crd
 '''Synopsis'''
-<span style="color: maroon;">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>
+<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'''
-Converts AMBER topology and coordinates to coordinates in other format.
+<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: 75%;"
+{| style="margin-left: 2em; width: 95%;"
 |- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">PARM</span><br/>
+| <span style="color: purple;">PARM</span><br/><div style="margin-left: 30px;">topology file name</div>
-<span style="margin-left: 30px;">topology file name</span>
 |- style="vertical-align: top;"
-| <span style="color: purple;">CRD</span><br/>
+| <span style="color: purple;">CRD</span><br/><div style="margin-left: 30px;">input coordinates file name or - for standard input</div>
-<span style="margin-left: 30px;">input coordinates file name or - for standard input</span>
 |- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">OUT</span><br/>
+| <span style="color: purple;">OUT</span><br/><div style="margin-left: 30px;">output coordinates file name or - for standard output</div>
-<span style="margin-left: 30px;">output coordinates file name or - for standard output</span>
 |}
@@ Line 31: / Line 29: @@
 {| style="margin-left: 2em; width: 95%;"
 |- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-i, --input FORMAT</span><br/><span style="margin-left: 30px;">specify input format for coordinates:
+|<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>
-   <green>crd</green>  - amber restart file
+|- style="vertical-align: top;"
-   <green>xyz</green>  - xyz file
+|<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>
-</span><br/><span style="color:purple; margin-left: 30px;">(Default: crd)</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;">-o, --output FORMAT</span><br/><span style="margin-left: 30px;">specify output format for coordinates:
+|<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>
-   <green>crd</green>        - amber restart file
-   <green>pdb</green>        - PDB file
-   <green>pqr</green>        - PDB file with atomic radii and charges
-   <green>xyz</green>        - xyz file
-   <green>xyzr</green>       - xyz file with atomic radii
-   <green>com</green>        - gaussian input file
-   <green>rbox</green>       - rbox format for qhull
-   <green>traj</green>       - amber trajectory file
-   <green>adf</green>        - plain ADF input
-   <green>adffrag</green>    - plain ADF input with one fragment
-   <green>adf3drism</green>  - plain ADF input for 3D-RISM</span><br/><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/><span style="margin-left: 30px;">only atoms selected according to MASK will be converted. Mutually exclusive with 'maskfile' option.</span><br/><span style="color:purple; margin-left: 30px;">(Default: )</span>
+|<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;">-f, --maskfile MASKFILE</span><br/><span 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.</span><br/><span style="color:purple; margin-left: 30px;">(Default: )</span>
+|<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/><span style="margin-left: 30px;">specify atom names mangling scheme:
+|<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>
-   <green>none</green>   - no translation (1234)
-   <green>pdb</green>    - pdb scheme (4123), keep amber names
-   <green>charmm</green> - charmm name scheme (1234), mangle parm99 names
-</span><br/><span style="color:purple; margin-left: 30px;">(Default: pdb)</span>
 |- style="vertical-align: top;"
-|<span style="color: blue;">--rscale</span><br/><span style="margin-left: 30px;">scale factor for atomic radii (r_new = r * scale + offset)</span>
+|<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/><span style="margin-left: 30px;">offset for atomic radii (r_new = r * scale + offset)</span>
+|<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/><span style="margin-left: 30px;">reindex atom and residue numbers counting from 1</span>
+|<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/><span style="margin-left: 30px;">copy box information to output file</span>
+|<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/><span style="margin-left: 30px;">do not transfer velocities</span>
+|<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/><span style="margin-left: 30px;">do not print chain IDs into pdb files</span>
+|<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/><span style="margin-left: 30px;">increase output verbosity</span>
+|<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/><span style="margin-left: 30px;">output version information and exit</span>
+|<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/><span style="margin-left: 30px;">display this help and exit</span>
+|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
 |}

Topcrd2crd: Difference between revisions

Latest revision as of 22:32, 3 March 2020

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