PRIMADORAC program reads a PDB of a molecule, typically a ligand, and
produces the associated ORAC topology (tpg) file. Atom-types
assignment is done according to the gaff2003 force field 
( see http://ambermd.org/antechamber/gaff.html for documentation).[1]
    
To compile the program cd into the src directory and do 

> make

To run the program on a test.pdb file, just do 

> PATH/primadorac < test.pdb 

The code will produce a lig.pdb , lig.tpg and lig.log output file containing
the pdb coordinates with the new atomic labels (lig.pdb) and the associated
topology file (lig.tpg). The log file "lig.log" contains essential info for
atomic assignment. 



[1] ESP charges must be computed independently and must provided in
the input PDB file. Expected format of the input PDB file is:
A30,3f8.3,f13.6 [string, x,y,x, esp_charge].  

You can also use the script "primadorac.bash" in this directory to
produce the topology and the related pdb file. "primadorac.bash" is a
wrapper that computes the AM1-BCC charges for the PDB file using mopac7
and then evaluate the ORAC topology file using primadorac for type
assignment. mopac7 is provided in this distribution as a compressed tar
archive. mopac7 is a public domain software and is distributed with the following
licence: 

      'This computer program is a work of the United States
       Government and as such is not subject to protection by
       copyright (17 U.S.C. # 105.)  Any person who fraudulently
       places a copyright notice or does any other act contrary
       to the provisions of 17 U.S. Code 506(c) shall be subject
       to the penalties provided therein.  This notice shall not
       be altered or removed from this software and is to be on
       all reproductions.'


To run primadorac.bash you must untar and install mopac you must have
installed the following packages:

1) g++
2) gfortran 
3) f2c 
4) openbabel 


