PolyParGen Manual

PolyParGen provides OPLS-AA and Amber force field parameters for polymers or large molecules. In the case that PolyParGen generates OPLS-AA parameters, PolyParGen leverages LigParGen [2] and BOSS [3]. On the other hand, PolyParGen leverages Antechamber [4] and ACPYPE [5] to make Amber parameters. If users want to use the atomic charge of ab initio calculation, user just select the option of ab initio calculation. Ab initio software is NWChem [6].

This site shows how to use the PolyParGen.

Content

• 1. Usage
  • 1.1. Make Molecular Parameter
    • 1.1.1. Upload File
    • 1.1.2. Draw Molecule
  • 1.2. Make Molecule

References

• [1] M. Yabe, K. Mori, K. Ueda, M. Takeda, J. Comput. Chem. Jpn. Int. Ed. 5, 2018-0034 (2019)

• [2] Dodda, L. S.; Cabeza de Vaca, I.; Tirado-Rives, J.; Jorgensen, W. L. Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W331-W336

• [3] Jorgensen, W. L.; Tirado-Rives, J. J. Comput. Chem. 2005, 26, 1689-1700. doi:10.1002/jcc.20297

• [4] Wang J, Wang W, Kollman PA, Case DA, Journal of Molecular Graphics and Modelling 25 (2):247-260 (2006)

• [5] Sousa da Silva AW, Vranken WF, BMC Research Notes 5:367-367 (2012)

• [6] M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha, E. Apra, T.L. Windus, W.A. de Jong, Comput. Phys. Commun. 181, 1477 (2010)