- 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.
It can create polymers with any chain length!
- Tacticity supported
- PMMA (T)
- PS (T)
- PE (T)
- PI (cis)
- PP (T)
- PVA (T)
Install AutoPoly via pip:
pip install AutoPolyLoad package AutoPoly in python script
import AutoPoly# 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:
# 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 data is created by Avogadra [https://avogadro.cc/]
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)"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
- Support coarse-grained polymers
- Support branched polymers
- Support ring polymers
- Support pre-relaxation using LAMMPS
- Integrate LigParGen for small molecules
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