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<TITLE>Solvate</TITLE>
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<h3>Solvate <img src="solvateicon.png" alt="Solvate icon"></h3>
<table align="right" style="margin:8px 8px 8px 8px">
<tr><td><img src="solvate.png" alt="1gcn in solvent box"></td></tr>
</table>
<p>
<b>Solvate</b> adds solvent around molecule models using
<a href="http://ambermd.org/#AmberTools" target="_blank">AmberTools</a>.
Thanks to Wei Zhang (The University of Texas Health Science Center at Houston)
for implementing this tool. See also:
<a href="../addions/addions.html"><b>Add Ions</b></a>,
<a href="../addions/writeprmtop.html"><b>Write Prmtop</b></a>
</p><p>
There are <a href="../../UsersGuide/extension.html">several ways to start</a>
<b>Solvate</b>, a tool in the <b>Structure Editing</b> and <b>Amber</b>
categories. It is also implemented as the command
<a href="../../UsersGuide/midas/solvate.html"><b>solvate</b></a>.
</p><p>
The model of interest should be chosen from the list.
Multiple models can be chosen, but they will be considered
individually rather than as a combined system.
</p><p>
Solvent addition requires explicit hydrogens.
If the molecule model does not include hydrogens,
a dialog for running <a href="../addh/addh.html"><b>AddH</b></a>
beforehand will appear.
</p><p>
<b>Solvate method</b> options:
<ul>
<li><b>Box</b> - rectangular box with edges no closer than
<b>Box size</b> (Å) to any atom in the solute
<li><b>Cap</b> - spherical cap with the specified
<b>Cap center</b> and <b>Cap Radius</b> (Å).
The center can be:
<ul>
<li> a residue identified by a number which is the residue ID
<li> an atom identified by a string like <b>ddd.xxx</b>, where
<b>ddd</b> is the residue ID and <b>xxx</b> is the name of the atom
</ul>
<li><b>Oct</b> - truncated octahedron with edges no closer than
<b>Oct size</b> (Å) to any atom in the solute
<li><b>Shell</b> - a layer of solvent extending <b>Shell extent</b> (Å)
from the solute. The shell will be irregular in shape since it
reflects the contours of the solute.
</ul>
The <b>Solvent Model</b> can be any of the following:
<ul>
<li><b>CHCL3BOX</b> - chloroform
<li><b>MEOHBOX</b> - methanol
<li><b>NMABOX</b> - N-methylacetamide
<li><b>POL3BOX</b> - POL3 water model
<li><b>QSPCFWBOX</b> - qSPC/Fw water model
<li><b>SPCBOX</b> - SPC/E water model
<li><b>SPCFWBOX</b> - SPC/Fw water model
<li><b>TIP3PBOX</b> - TIP3P water model
<li><b>TIP3PFBOX</b> - TIP3P/F water model
<li><b>TIP4PBOX</b> - TIP4P water model
<li><b>TIP4PEWBOX</b> - TIP4P/Ew water model
</ul>
One can <b>Remove existing ions/solvent</b> (recommended) before
solvating the system. The affected atoms are those
<a href="../../UsersGuide/midas/surface.html#surfcats">automatically
classified</a> by Chimera as <b>ions</b> and <b>solvent</b>.
Partial charges corresponding to the chosen solvent model will be assigned
as the <a href="../defineattrib/defineattrib.html#attribdef">attribute</a>
named <b>charge</b> to atoms in the existing (if not removed)
and newly added solvent residues.
The process of solvation may move (translate) the structure.
</p><p>
<b>OK</b> initiates adding solvent and dismisses the panel,
while <b>Apply</b> adds solvent without dismissing the panel.
Addition may take several seconds; progress is reported in the
<a href="../../UsersGuide/chimerawindow.html#statusline">status line</a>.
<b>Close</b> dismisses the panel without adding any solvent.
<b>Help</b> brings up this manual page in a browser window.
</p><p>
See the
<a href="http://ambermd.org/#AmberTools" target="_blank">AmberTools</a>
documentation for further details.
</p>
<hr>
<address>UCSF Computer Graphics Laboratory / June 2009</address>
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