RECON Help Window

Installation

How to run the GUI

RECON Manual

Installation:

• Unzip the archive into the C: drive. The software will then be installed in C:\RECON6-3 and the atomic data files into a directory DATA under that. This directory structure is mandatory.
• If not already installed on your computer, download java version 1.2 or later.

  The batch file C:\RECON5-3\RECON.BAT enables the WinRecon GUI to be run as a single command from a DOS shell or from the Run dialog box in the Start Menu. The batch file C:\RECON6-3\INSTALL.BAT compiles the java files. These file assumes that java is located in the directory C:\jdk\bin
  If you have installed java in a different directory, edit the C:\RECON5-3\RECON.BAT and C:\RECON6-3\INSTALL.BAT files to reflect the actual location of java.

• Compile the java classes by double-clicking on INSTALL.BAT iconin the C:\RECON5-3 folder.

recon6-3.exe can also be run without the GUI from a DOS shell or by double clicking the executable icon; if this option is used, the input is read from the file recon.inp in the C:\RECON6-3 directory.

How to run the GUI:

1. Double-click on RECON.BAT to launch the Java GUI for WinRECON
2. Select the Configure Option
3. In the Configure Panel, first select the input file type in the File Menu.
4. If you enter an interactive SMILES string instead, skip now to step 7
5. Open the File Menu (in the Configure Panel), click on "Add Files" and select your molecular files from any directory
6. If you want to select any other non-default options from the other menus, do so at this time
7. Click on Save to save your options and file selections
8. Select the Run Option
9. When WinRECON completes execution, you can view the output files (recon.ff and recon.stt), when prompted, in the Notepad

RECON Manual

Current Limitations:

The output summary files recon.ff (TAE descriptors), recon.stt (atom type visitation statistics) and recon.err (atom type mismatch log) are, by default, saved to the C:\RECON5-5 directory. Use the "Save As" option in the Notepad to save them elsewhere.

Note that the rpdb algorithm of the current version of recon5-5 requires ALL atoms (including Hydrogens) to be explicitly listed in the ATOM/HETATM records of the pdb file and ALL bonds to be explicitly listed in the BOND/CONECT records of the pdb file.

Please report bugs or comments to:

• Dr. N. Sukumar    (518)276-2835
• Prof. Curt Breneman  (518)276-2678