The following documents the procedure for submitting new entries into the DFT Database for RNA Catalysis.  Currently, this is only allowed for York Group members and their collaborators that have accounts on our server and CVS access.  All new entries must follow the "last line of defense" protocol, and must be submitted to the database manager (Yun Liu) for final upload.

There are a number of helpful script files located in the CVS directory tree available to York Group members and their collaborators in:



The "Last-line-of-defense" (LLOD) procedure

The LLOD procedure was designed to ensure a strict protocol for all quantum calculations scheduled for upload into the database.  The process begins with a Gaussian03 output file that is processed by a Perl script "gauss2everything.pl" (located in DataBase/Semiempirical-SRP/Utilities/EXE) to produce a new Gaussian03 Input file that contains all of the instructions to run geometry optimization, frequency calculations, wave function stability checks, high-level single-point energy refinement, and solvations calculations including specialized output formatting flags for visualization using MOLDEN.


Submitting Gaussian03 LLOD Output Files to the Database

The procedure for submitting Gaussian LLOD Output files to be scheduled for upload into the Database is as follows:

• Run the complete LLOD procedure with Gaussian03
• Check to make certain that the job has completed successfully in it's entirety
• Create a single appropriately named Output file
• Commit the output file in CVS to:

• The files will then be scheduled for the next upload by Yun into the Database