Author: Israel Cabeza de Vaca Lopez Email: israel.cabezadevaca@yale.edu // israel.cabezadevaca@icm.uu.se Place: William L. Jorgensen Lab at Yale University // Jens Carlsson Lab at Uppsala university Date: 2020-2021
Description: An automatic OPLS-AA parameter generator for small organic molecules using CM1A, 1.14CM1A and CM1A-LBCC charge models. LigParGen accepts any Open Babel molecular format including SMILES, PDB, MOL, MOL2, among others. Final OPLSAA parameter outputs will be written in topology/coordinate input files for BOSS, Q, Tinker, PQR, openMM, CHARMM/NAMD, Gromacs, LAMMPS, Desmond, and xplor softwares.
Note: This new version has been written from scratch but it is based on the Leela Dodda initial ligpargen python code.
New LigParGen features:
LigParGen requires the free BOSS software to generate the OPLSAA parameters.
1 - Download and install BOSS software from the official William L. Jorgensen lab website: http://zarbi.chem.yale.edu/software.html
BOSS is compiled for linux using 32 bits libraries so it can not run in windows using WSL. Alternatively, you can use a virtual machine in windows such as virtualBox to install a linux distro (ubuntu, centos, ...) and run LigParGen.
1.1 - Set the BOSSdir enviromental variable:
bashrc
export BOSSdir=PATH_TO_BOSS_DIRECTORY
cshrc
setenv BOSSdir PATH_TO_BOSS_DIRECTORY
TIP: add this command line in your ~/.bashrc or ~/.cshrc file.
2 - Download and install conda (anaconda or minicoda):
wget https://repo.anaconda.com/archive/Anaconda3-2020.11-Linux-x86_64.sh
or
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
3 - Create and activate an enviroment for python3.7 (Everything was tested with 3.7):
conda create --name py37 python=3.7
conda activate py37
Optional TIP: add this line to your .bashrc/.cshrc,....
4- Install rdkit and openbabel in py37 enviroment
conda install -c rdkit rdkit
conda install -c conda-forge openbabel
5 - Download and install LigParGen
git clone https://github.com/Isra3l/ligpargen.git
pip install -e ligpargen
Optional: Check your installation by runing the tests included in the ligpargen folder.
cd ligpargen;python -m unittest test_ligpargen/test_ligpargen.py
TIP: Do not forget to activate your py37 enviroment before using LigParGen.
conda activate py37
Input arguments list:
For alchemical transformations:
Notes:
Molecule template generation:
ligpargen -i phenol.pdb -n phenol -p phenol -r MOL -c 0 -o 0 -cgen CM1A
ligpargen -s 'c1ccc(cc1)O' -n phenol -p phenol -r MOL -c 0 -o 0 -cgen CM1A
ligpargen -s 'c1ccc(cc1)O'
ligpargen -s 'c1ccc(cc1)O' -n phenol -cgen CM1A-LBCC
Alchemical transformations:
ligpargen -i phenol.pdb -ib benzene.pdb -n phenolToBenzene -p phenol2bnz -r A2B -c 0 -o 0 -cgen CM1A -cb 0 -ob 1 -cgenb CM1A-LBCC
ligpargen -i phenol.pdb -ib benzene.pdb -n phenolToBenzene
ligpargen -s 'c1ccc(cc1)O' -sb 'c1ccccc1' -n phenol_benzene
ligpargen -s 'c1ccc(cc1)O' -sb 'c1ccccc1' -n phenol_benzene -o 0 -cgen CM1A -cb 0 -ob 1 -cgenb CM1A-LBCC
ligpargen -i phenol.pdb -sb 'c1ccccc1' -n phenol_benzene -o 0 -cgen CM1A -cb 0 -ob 1 -cgenb CM1A-LBCC
Default values:
For help use the -h flag:
ligpargen -h
Please do not forget to cite the following references:
LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands
Leela S. Dodda Israel Cabeza de Vaca Julian Tirado-Rives William L. Jorgensen
Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W331–W336
1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations