LigParGen

Release 2.1

Python script to provide BOSS generated OPLS-AA/CM1A(-LBCC) parameters for organic molecules and ligands.

Homepage PyPI

Keywords
computational, chemistry
License
MIT
Install
pip install LigParGen==2.1

Documentation

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:

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?

Stats

Dependencies
0
Dependent packages
0
Dependent repositories
0
Total releases
7
Latest release
First release
Forks
0
Watchers
1
Contributors
0
Repository size
491 KB
SourceRank
6

Development practices

Source repo 2FA enabled
TEXT!
Package manager 2FA enabled
TEXT!
Is security responsive
TEXT!
Dependencies are managed
TEXT!
Issue-free release available
TEXT!
Succession plan available
TEXT!
Package manager 2FA enabled
TEXT!

The Tidelift Subscription provides access to a continuously curated stream of human-researched and maintainer-verified data on open source packages and their licenses, releases, vulnerabilities, and development practices.

Learn more →

Releases

2.1
0.15
0.14
0.13
0.12
0.11
0.10

Something wrong with this page? Make a suggestion

Export .ABOUT file for this package

Last synced: 2021-02-17 11:48:17 UTC

Login to resync this project