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:
DataBase/Semiempirical-SRP/Utilities/EXE
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:
DataBase/Semiempirical-SRP/DataBase/DB2_B3LYP.B1/Incoming
- The files will then be
scheduled for the next upload by Yun into the Database