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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:

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

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