LigParGen_2.3

Python package to convert BOSS generated OPLS-AA/CM1A(-LBCC) & OPLS-AA/CM5 parameters to:

• OpenMM PDB AND XML FILES,
• CHARMM RTF AND PRM FILES,
• Gromacs/NAMD ITP AND GRO FILES,
• PDB2PQR PQR FILES,
• MCPRO & BOSS ZMATRIX
• LAMMPS lmp and data FILES
• tinker xyz and key files
• .Q.param and lib files for package Q
• Desmond cms file

Whats New ?

** OPLS-AA/CM5 FF parameters with ORCA log file as input **

authors:

• Leela S. Dodda - <leela.dodda@yale.edu>
• Israel Cabeza de Vaca - <israel.cabezadevaca@yale.edu>
• Ayan Bhattacharjee - <abhattacharjee.me@gmail.com>
• Matt Robinson

REQUIREMENTS:

• BOSS (need to set BOSSdir in bashrc and cshrc)
• Preferably Anaconda python with following modules
• pandas
• argparse
• numpy
• openbabel (for 2D to 3D conversion)
• RDKit for CM5 charges

Installation instructions

# Conda provides an easy way to install rdkit
conda install -c rdkit rdkit
python setup.py install

Usage

if using BOSS Zmat: LigParGen -z phenol.z -r PHN -c 0 -o 0 -l

if using MOL file: LigParGen -m phenol.mol -r PHN -c 0 -o 0 -l

if using PDB file: LigParGen -p phenol.pdb -r PHN -c 0-o 0 -l

if using BOSS SMILES CODE: LigParGen -s 'c1ccc(cc1)O' -r PHN -c 0 -o 0 -l

Who do I talk to?

• Leela S. Dodda leela.dodda@yale.edu
• Israel Cabeza de Vaca
• Matthew Robinson