PURPOSE: This protocol is a modified version of the standard "Solvation" protocol. In this protocol only the Explicit Periodic Boundary method is used and the "COOR ORIE" statement is removed from the CHARMm script so that the solute molecule is not automatically recentered and reoriented by the protocol prior to adding solvent.
The Center to Origin parameter provides an option to translate the center of mass of the molecule to the origin.
Note, the solvent box is always built around the origin therefore if the solute molecule's center is far from the origin it will not appear in the center of the solvent box or in some cases no solvent will be generated at all.

USAGE: This protocol can be launched from both the Discovery Studio and Pipeline Pilot clients. To install in Discovery Studio only, go to the Protocol Explorer, right-click over the folder you want to add the protocol to, choose Import, navigate to the location of the Solvation Explicit Periodic Boundary (no reorienting).xml file and enter it as the File Name.

REQUIREMENTS: Discovery Studio Embedded Collection, CHARMm

KEYWORDS: solvation, centering, reorienting, solute coordinates

DISCLAIMER: This custom protocol is compatible with Discovery Studio 2.1 and Pipeline Pilot Server versions 6.1.6 and 7.0.1 (SES). It is provided "as is" and is NOT supported by Accelrys nor is it warranted for any purpose whatsoever. The user assumes responsibility for any malfunctions or bugs.