AutoPoly.py: Automatic Generation of Data File for Polymers

• Support OPLS (Optimized Potentials for Liquid Simulations) force field that was developed by Prof. William L. Jorgensen at Purdue University and later at Yale University.

Why AutoPoly?

It can create polymers with any chain length!

Version update

• Tacticity supported

Support Polymers

1. PMMA (T)
2. PS (T)
3. PE (T)
4. PI (cis)
5. PP (T)
6. PVA (T)

How to use AutoPoly.py?

Install AutoPoly via pip:

pip install AutoPoly

Load package AutoPoly in python script

import AutoPoly

Create polymer system with PP PE chains at AA, UA levels

# Define the system
# out is the folder name for the output
system=AutoPoly.System(out="test")

# create polymers
# Just an example of polypropylene and polyethylene with all-atom and united-atom resolutions
PPUA=AutoPoly.Polymer(ChainNum=2,Sequence=["PPUA"]*20)
PEUA=AutoPoly.Polymer(ChainNum=2,Sequence=["PEUA"]*10)
PEAA=AutoPoly.Polymer(ChainNum=3,Sequence=["PEAA"]*15)

# polymerization
# Name is the output folder for this polymer
poly=AutoPoly.Polymerization(Name="Polymer",System=system,Model=[PPUA,PEUA,PEAA],run=True)

you will get something looks like this using Visual Molecular Dynamics:

Create molecular system with 50 benzenes

# Define the system
# out is the folder name for the output
system=AutoPoly.System(out="test_molecule")

# create polymers
# Just an example of benzene with all-atom resolutions
benzene=AutoPoly.Polymer(ChainNum=50,Sequence=["Benzene"])

# polymerization
# Name is the output folder for this polymer
poly=AutoPoly.Polymerization(Name="Benzene",System=system,Model=[benzene],run=True)

you will get something looks like this using Visual Molecular Dynamics:

Monomer Bank

Monomer data is created by Avogadra [https://avogadro.cc/]

RDkit

AutoPoly supports create molecules from RDkit directly and store them in monomer_bank for future use

rdlt=AutoPoly.RDlt(smiles='c1c2ccccc2ccc1')
rdlt.run(to_file='Naphthalene.lt')
rdlt.store_bank()# flag=True/False to store or not in the monomer bank, default: True

# Define the system
# out is the folder name for the output
system=AutoPoly.System(out="test_molecule_from_RDkit")

# create polymers
# Just an example of naphthalene with all-atom resolutions
naphthalene=AutoPoly.Polymer(ChainNum=50,Sequence=["Naphthalene"])

# polymerization
# Name is the output folder for this polymer
poly=AutoPoly.Polymerization(Name="Naphthalene",System=system,Model=[naphthalene],run=True)

Acknowledge

"Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics", J. Mol. Biol., 2021, 433(11):166841, Jewett AI, Stelter D, Lambert J, Saladi SM, Roscioni OM; Ricci M, Autin L, Maritan M, Bashusqeh SM, Keyes T, Dame RT; Shea J-E, Jensen GJ, Goodsell DS https://doi.org/10.1016/j.jmb.2021.166841

"rdlt": Script to automate assignment of atom types and build .lt files for use with moltemplate and the OPLS and L-OPLS forcefields that come packaged with it. https://github.com/asteeves/rdlt

To-do list

• Support coarse-grained polymers
• Support branched polymers
• Support ring polymers
• Support pre-relaxation using LAMMPS
• Integrate LigParGen for small molecules