pdbNAMDRestraintCreate - Revision history

Kinoshita: Created page with "'''pdbNAMDRestraintCreate''' is Eos's Command that creates the data for NAMD from PDB file. == List of option == === Main option === ..."
2014-08-08T01:30:34Z
Created page with "'''pdbNAMDRestraintCreate''' is Eos's Command that creates the data for NAMD from PDB file. == List of option == === Main option === <table border="1">..."
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'''pdbNAMDRestraintCreate''' is [[Eos]]'s [[Command]] that creates the data for [[NAMD]] from [[PDB]] file.

== 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>-r</td>
<td>Essential</td>
<td>Reference: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: NAMD Restraint</td>
<td>stdout</td>
</tr>
<tr>
<td>-O</td>
<td>Optional</td>
<td>Output: PDB Force</td>
<td>stdout</td>
</tr>
<tr>
<td>-kf</td>
<td>Optional</td>
<td>Input: Kf kcal/mol/A^2</td>
<td>1.0</td>
</tr>
<tr>
<td>-autokf</td>
<td>Optional</td>
<td>Input: Kf kcal/mol for averaged length</td>
<td>1.0</td>
</tr>
<tr>
<td>-seg</td>
<td>Optional</td>
<td>Input: segment name</td>
<td>EXAMPLE</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>

<div>-autokf is prior to -kf.</div>
<br>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>
<br>

== Execution example ==
===[[:Media:Input-121P-T1.pdb.zip|Input file]] image===
<table>
<tr>
<td>[[File:Input-121P-PDB1.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 9.408175e+00 2.622422e+01<br>
3.286665e+01<br>
24.77 22.88 23.78<br></p>
</td>
</tr>
</table>
<br>

===[[:Media:Input-121P.pdb.zip|Reference 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>-o 's data</div>
<pre>
urestraint {
posi (EXAMPLE,1,ca) kf=1 ref=(-5.913,31.928,-6.676)
posi (EXAMPLE,2,ca) kf=1 ref=(-4.759,28.93,-4.751)
posi (EXAMPLE,3,ca) kf=1 ref=(-4.531,29.674,-1.062)
posi (EXAMPLE,4,ca) kf=1 ref=(-2.465,27.513,1.336)
posi (EXAMPLE,5,ca) kf=1 ref=(-3.586,27.58,4.978)

...

posi (EXAMPLE,162,ca) kf=1 ref=(3.951,18.742,0.732)
posi (EXAMPLE,163,ca) kf=1 ref=(0.404,20.135,0.49)
posi (EXAMPLE,164,ca) kf=1 ref=(0.711,20.05,-3.346)
posi (EXAMPLE,165,ca) kf=1 ref=(1.52,16.308,-3.145)
posi (EXAMPLE,166,ca) kf=1 ref=(-1.217,15.28,-0.638)
}
</pre>
<br>

<div>-O 's data</div>
<table>
<tr>
<td>[[File:Outdata-pdbNAMDRestraintCreate.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">0.000000e+00 1.578772e+01 -1.433346e+01<br>
2.132370e+01<br>
0.00 15.79 14.33<br> </p>
</td>
</tr>
</table>
<br>

=== Option -kf===
====Case: kf=2====
<div>-o 's data</div>
<pre>
urestraint {
posi (EXAMPLE,1,ca) kf=2 ref=(-5.913,31.928,-6.676)
posi (EXAMPLE,2,ca) kf=2 ref=(-4.759,28.93,-4.751)
posi (EXAMPLE,3,ca) kf=2 ref=(-4.531,29.674,-1.062)
posi (EXAMPLE,4,ca) kf=2 ref=(-2.465,27.513,1.336)
posi (EXAMPLE,5,ca) kf=2 ref=(-3.586,27.58,4.978)

...

posi (EXAMPLE,162,ca) kf=2 ref=(3.951,18.742,0.732)
posi (EXAMPLE,163,ca) kf=2 ref=(0.404,20.135,0.49)
posi (EXAMPLE,164,ca) kf=2 ref=(0.711,20.05,-3.346)
posi (EXAMPLE,165,ca) kf=2 ref=(1.52,16.308,-3.145)
posi (EXAMPLE,166,ca) kf=2 ref=(-1.217,15.28,-0.638)
}
</pre>
<br>

<div>-O 's data</div>
<table>
<tr>
<td>[[File:Outdata-kf-pdbNAMDRestraintCreate.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">0.000000e+00 3.157545e+01 -2.866693e+01<br>
4.264741e+01<br>
0.00 31.58 28.67<br> </p>
</td>
</tr>
</table>
<br>

=== Option -autokf===
====Case: autokf=2====
<div>-o 's data</div>
<pre>
urestraint {
posi (EXAMPLE,1,ca) kf=0.186306 ref=(-5.913,31.928,-6.676)
posi (EXAMPLE,2,ca) kf=0.186306 ref=(-4.759,28.93,-4.751)
posi (EXAMPLE,3,ca) kf=0.186306 ref=(-4.531,29.674,-1.062)
posi (EXAMPLE,4,ca) kf=0.186306 ref=(-2.465,27.513,1.336)
posi (EXAMPLE,5,ca) kf=0.186306 ref=(-3.586,27.58,4.978)

...

posi (EXAMPLE,162,ca) kf=0.186306 ref=(3.951,18.742,0.732)
posi (EXAMPLE,163,ca) kf=0.186306 ref=(0.404,20.135,0.49)
posi (EXAMPLE,164,ca) kf=0.186306 ref=(0.711,20.05,-3.346)
posi (EXAMPLE,165,ca) kf=0.186306 ref=(1.52,16.308,-3.145)
posi (EXAMPLE,166,ca) kf=0.186306 ref=(-1.217,15.28,-0.638)
}
</pre>
<br>

<div>-O 's data</div>
<table>
<tr>
<td>[[File:Outdata-autokf-pdbNAMDRestraintCreate.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">0.000000e+00 2.941331e+00 -2.670398e+00<br>
3.972714e+00<br>
0.00 2.94 2.67<br> </p>
</td>
</tr>
</table>
<br>

=== Option -seg===
====Case: seg=SEGNAME====
<div>-o 's data</div>
<pre>
urestraint {
posi (SEGNAME,1,ca) kf=1 ref=(-5.913,31.928,-6.676)
posi (SEGNAME,2,ca) kf=1 ref=(-4.759,28.93,-4.751)
posi (SEGNAME,3,ca) kf=1 ref=(-4.531,29.674,-1.062)
posi (SEGNAME,4,ca) kf=1 ref=(-2.465,27.513,1.336)
posi (SEGNAME,5,ca) kf=1 ref=(-3.586,27.58,4.978)

...

posi (SEGNAME,162,ca) kf=1 ref=(3.951,18.742,0.732)
posi (SEGNAME,163,ca) kf=1 ref=(0.404,20.135,0.49)
posi (SEGNAME,164,ca) kf=1 ref=(0.711,20.05,-3.346)
posi (SEGNAME,165,ca) kf=1 ref=(1.52,16.308,-3.145)
posi (SEGNAME,166,ca) kf=1 ref=(-1.217,15.28,-0.638)
}
</pre>
<br>