LigParGen server 2.0

Python script to convert BOSS generated OPLS-AA/CM1A(-LBCC) parameters to:

• OPENMM PDB AND XML FILES,
• CHARMM RTF AND PRM FILES,
• GROMACS ITP AND GRO FILES,
• PDB2PQR PQR FILES,
• MCPRO & BOSS ZMATRIX

authors:

• Leela S. Dodda - <leela.dodda@yale.edu>
• Matt Robinson - <matthew.robinson@yale.edu>

Usage

if using BOSS Zmat: python Converter.py -z phenol.z -r PHN -c 0

if using MOL file: python Converter.py -m phenol.mol -r PHN -c 0

if using PDB file: python Converter.py -p phenol.pdb -r PHN -c 0

if using BOSS SMILES CODE: python Converter.py -s 'c1ccc(cc1)O' -r PHN -c 0

To ensure your version is working, cd into the tests/ folder and run the following: python run_ligpargen_regression_tests.py

REQUIREMENTS:

• BOSS (need to set BOSSdir in bashrc and cshrc)
• Preferably Anaconda python with following modules
• pandas
• argparse
• numpy
• RDKit for using with SMILES code

Additionally you must make changes to the following BOSS scripts

• xZCM1A
  • comment out everything after first single point calculation
• xMOLZ
  • change default to varadd in the line, $BOSSdir/autozmat -i mdl -z default <${argv[1]}.mol >${argv[1]}.z
• xPDBZ
  • same as for xMOLZ

What more to do ?

• Fix issues with Linear Molecules (Fixed)
• Create BOSS2LAMMPS (IC)
• Create BOSS2Q (LSD??)
• Create BOSS2AMBER (JTR)
• Create Halogen bond extra site feature
• ** Create RelFEP setup for BOSS, MCPro, Gromacs and NAMD (Code is done by LSD & MR)**
• Include RelFEP in server as Alchemist ?? (IC)

Who do I talk to?

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