parafreq version 1.1 README
===================

The program 'parafreq' computes force constants for AMBER force fields based on the QM frequencies.
The software is the same used in the article:
"Automated Parametrization of AMBER Force Field Terms from Vibrational Analysis with a Focus on Functionalizing Dinuclear Zinc(II) Scaffolds" 
J. Chem. Theory Comput., 2012 , Article DOI: 10.1021/ct2007742

License
-------

'parafreq' is distributed as open source software under the conditions of the GPL
license.  Read the file COPYING for more details, or visit
http://www.gnu.org/licenses/

Software dependencies
---------------------

The following software has to be installed on your system before you can use
Tracks:
 1) Python (>=2.4, <3.0): see http://www.python.org/
 2) Numpy (>=1.0.1): see http://www.scipy.org/

Example using model II from J. Chem. Theory Comput. 2010, 6, 1852-1870
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Steps

1) g09 FREQ calculation using HF/6-31G* using chk=sm4.chk in the header section.

2) Convert .chk file to .fchk file and generate .pdb and .xyz files.
e.g. $g09root/formchk ~/g98/sm_test/sm4.chk

./log_to_pdb.pl model_II.log > model_II.pdb # 
./log_to_xyz.pl model_II.log > model_II.xyz # add END to the bottom of file.

3) Parameterize the ligand with antechamber.

antechamber -i model_II.pdb -fi pdb -o model_II.mol2 -fo mol2

python add_charge_mol2.py model_II.mol2 model_II.log  -fi log # quick way to add the charges from the .log file.

cp out.mol2 charge.mol2 # check the charges and then replace the original file.
python add_bonds_to_zn.py charge.mol2  # generates out.mol2

parmchk -i model_II.mol2 -a 'Y' -f mol2 -o all.frcmod 
parmchk -i model_II.mol2 -f mol2 -o model_II.frcmod 

# put the dihedral and improper terms into extra.frcmod. These won't be determined by parafreq.

tleap -f leap.in
cp model_II.pdb hess.pdb

4) Iteratively generate the force constants 

# The NAB package comes packaged with AMBER and the
# a.out file can be compiled using with the command 'nab hess.nab'.

cp model_II.prmtop hess.prmtop
./a.out 2> hess.dat 
python para_freq.py model_II > terms
python find_terms.py terms model_II.mol2 model_II.frcmod > new.frcmod
cp new.frcmod model_II.frcmod
tleap -f leap.in

Redo (4) until the change in the force constants (terms) becomes small.


Contact information
-------------------

Main Supervisor:

Prof. Paul Ayers
Department of Chemistry and Chemical Biology, McMaster University
1280 Main St. West, Hamilton, Ontario
Canada
Email: ayers@mcmaster.ca


Author:

Dr. Steven K. Burger 
Department of Chemistry and Chemical Biology, McMaster University
1280 Main St. West, Hamilton, Ontario
Canada
Email: burgers@mcmaster.ca


