Kinoshita: Created page with "'''pdbWaterAdd''' is Eos's Command that adds water molecules around the input file. Output file is structured at water molecules only. == List of option == === Main..."

2014-08-18T02:00:14Z

Created page with "'''pdbWaterAdd''' is Eos's Command that adds water molecules around the input file. Output file is structured at water molecules only. == List of option == === Main..."

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'''pdbWaterAdd''' is [[Eos]]'s [[Command]] that adds water molecules around the input file. Output file is structured at water molecules only.

== List of option ==
=== Main option ===
<table border="1">
<tr>
<th>Option</th>
<th>Essential/Optional</th>
<th>Description</th>
<th>Default</th>
</tr>
<tr>
<td>-i</td>
<td>Essential</td>
<td>Input: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-d</td>
<td>Optional</td>
<td>Density of Water: [M]</td>
<td>55.55555</td>
</tr>
<tr>
<td>-r</td>
<td>Optional</td>
<td>Radius of Water Volume(for m=0, 1)</td>
<td>100</td>
</tr>
<tr>
<td>-height</td>
<td>Optional</td>
<td>Height of Water Volume(for m=1)</td>
<td>100</td>
</tr>
<tr>
<td>-cube</td>
<td>Optional</td>
<td>(X, Y, Z): [A](for m=3)</td>
<td>(100, 100, 100)</td>
</tr>
<tr>
<td>-edge</td>
<td>Optional</td>
<td>layer number(for m=2)</td>
<td>3</td>
</tr>
<tr>
<td>-c</td>
<td>Optional</td>
<td>ConfigurationFile</td>
<td>NULL</td>
</tr>
<tr>
<td>-m</td>
<td>Optional</td>
<td>Mode</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</table>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>sphere</td>
</tr>
<tr>
<td>1</td>
<td>cylinder</td>
</tr>
<tr>
<td>2</td>
<td>Edge</td>
</tr>
<tr>
<td>3</td>
<td>Cube</td>
</tr>
</table>

== Execution example ==
===[[:Media:Input-121P.pdb.zip|Input file]] image===
<table>
<tr>
<td>[[File:Input-121P-PDB.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">6.053012e+00 2.519590e+01 1.189075e+01<br>
3.286664e+01 <br>
24.77 23.85 28.04<br></p>
</td>
</tr>
</table>
<br>

=== Case: Options only essential ===
<div>White is Input file.</div>
<table>
<tr>
<td>[[File:Outdata-pdbWaterAdd.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">9.330483e+00 2.794594e+01 1.553714e+01<br>
1.010862e+02<br>
100.31 100.22 100.46<br></p>
</td>
</tr>
</table>
<br>

=== Option -r===
====Case: r=30====
<div>White is Input file.</div>
<table>
<tr>
<td>[[File:Outdata-r-pdbWaterAdd.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">1.013427e+01 2.852403e+01 1.641233e+01<br>
3.179522e+01 <br>
29.60 29.31 29.34<br> </p>
</td>
</tr>
</table>
<br>

=== Option -d===
====Case: d=100, r=30====
<div>White is Input file.</div>
<table>
<tr>
<td>[[File:Outdata-d-pdbWaterAdd.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">1.088372e+01 2.846397e+01 1.583489e+01<br>
3.126308e+01<br>
29.54 29.43 29.34<br></p>
</td>
</tr>
</table>
<br>

=== Option -m===
====Case: m=1====
=====Case: No other settings=====
<div>White is Input file.</div>
<table>
<tr>
<td>[[File:Outdata-m1-pdbWaterAdd.png]]<br>
<br>
[[File:Outdata-m1(yz)-pdbWaterAdd.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">9.336175e+00 2.794978e+01 1.554270e+01<br>
1.124455e+02<br>
100.48 100.40 51.18<br> </p>
</td>
</tr>
</table>
<br>

=====Case: height=50, r=30=====
<div>White is Input file.</div>
<table>
<tr>
<td>[[File:Outdata-m1height-pdbWaterAdd.png]]</td>
<td>[[File:Outdata-m1height(yz)-pdbWaterAdd.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">9.900170e+00 2.835893e+01 1.610196e+01<br>
3.983113e+01<br>
29.49 29.53 26.50<br> </p>
</td>
</tr>
</table>
<br>

====Case: m=2====
=====Case: No other settings=====
<div>White is Input file.</div>
<table>
<tr>
<td>[[File:Outdata-m2-pdbWaterAdd.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">2.902557e+00 2.626757e+01 1.201421e+01<br>
4.315685e+01<br>
32.09 31.73 33.16<br> </p>
</td>
</tr>
</table>
<br>

=====Case: edge=1=====
<div>White is Input file.</div>
<table>
<tr>
<td>[[File:Outdata-m2edge-pdbWaterAdd.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">3.767874e+00 2.603396e+01 1.347542e+01<br>
3.475105e+01<br>
25.49 26.98 29.59<br> </p>
</td>
</tr>
</table>
<br>

====Case: m=3====
=====Case: No other settings=====
<div>White is Input file.</div>
<table>
<tr>
<td>[[File:Outdata-m3-pdbWaterAdd.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">7.796508e+00 2.639248e+01 1.400760e+01<br>
8.374090e+01<br>
49.54 49.47 49.50<br> </p>
</td>
</tr>
</table>
<br>

=====Case: cube=(150, 50, 25)=====
<div>White is Input file.</div>
<table>
<tr>
<td>[[File:Outdata-m3cube-pdbWaterAdd.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">8.101933e+00 2.262963e+01 1.431665e+01<br>
4.112811e+01<br>
24.75 25.55 24.59<br> </p>
</td>
</tr>
</table>
<br>

pdbWaterAdd - Revision history

Kinoshita: Created page with "'''pdbWaterAdd''' is Eos's Command that adds water molecules around the input file. Output file is structured at water molecules only. == List of option == === Main..."