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

Usage

In the following it is shown how to use PolyParGen.

Make Molecular Parameter

In PolyParGen, Molecular parameters are generated by 2 methods. One of methods is uploading of molecular file. Another method is drawing a molecule. Users can select the method from them in PolyParGen front page.

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Upload File

This page shows how to make molecular mapameter from file uploading.

In the case that users want to make the molecular parameter from their own file, Users push the following image in PolyParGen front page.

Step1, users have to registrate their information to use PolyParGen. E-mail address certainly is needed in user’s informaiton, because PolyParGen sends that parameter file to user’s e-mail after generation of molecular parameter. The users, which already registrated, pass this step.

Step2, users upload the molecule file from the following buttom.

Note

The uploaded file format, which we recommend, is CML file format , because CML file format has more detail for each bond infromation. CML file can be generated by Avogadro or Open Babel .

Warning

• The current version can not apply for cation and anion molecule.

• Users have to add hydrogen atoms for molecules which are made without hydrogenation.

• 1 file have to set absolutely 1 molecule without solvent.

• Input files only supporte CML format. Aromatic notation is not supported, describe in single bond and double bond.

Step3, user setect the options for making molecular parameter.

This is the window of Step4.

• Select PolyParGen version

At present, the support of PolyParGen version 1 has been suspended to create accurate potential parameters. Users select PolyParGen version 2 (v2).

• Select the type of Lennard-Jones potential

Users select OPLS-AA or Amber parameter. In the case of Amber parameter, users select an atomic charge evaluation method (bcc or gas).

• Set the number of fragment’s atoms

Users set the number of atoms contained in one fragment. The default value is 150 atoms. Basically, the default value is recommended.

• Extra options

For large-scale conjugated molecules such as graphene and fullerene, users have to set “0”.

• Whether to evaluate atomic charges by ab initio calculation.

If users want to select the estimated atomic charge by ab initio calculation, users select this option. Also, users have to select the method, basis function and charge densith of method. ESP is the electrostatic potential fitting method. Mulliken is Mulliken density analysis.

Step4,Input the registrated e-mail address. After PolyParGen makes the moleculer parameter, the molecule’s parameter files are sent to the registrated e-mail address. Users have to input your e-mail.

Finaly, users push “Submit Molecule” button.

Draw Molecule

This page shows how to make molecular mapameter from the drawed molecule.

In the case that users want to make their drawed molecules, Users push the following image in PolyParGen front page.

Step1, users have to registrate their information to use PolyParGen. E-mail address certainly is needed in user’s informaiton, because PolyParGen sends that parameter file to user’s e-mail after generation of molecular parameter. The users, which already registrated, pass this step.

Step2, users draw a molecule under our drawer tool.

Step3, users confirm the drawn molecule in a 3D structure from with “generate 3D” button. If the molecule has a different structure, users draw the molecule again.

Step4, user setect the options for making molecular parameter.

This is the window of Step4.

• Select PolyParGen version

At present, the support of PolyParGen version 1 has been suspended to create accurate potential parameters. Users select PolyParGen version 2 (v2).

• Select the type of Lennard-Jones potential

Users select OPLS-AA or Amber parameter. In the case of Amber parameter, users select an atomic charge evaluation method (bcc or gas).

• Set the number of fragment’s atoms

Users set the number of atoms contained in one fragment. The default value is 150 atoms. Basically, the default value is recommended.

• Extra options

For large-scale conjugated molecules such as graphene and fullerene, users have to set “0”.

• Whether to evaluate atomic charges by ab initio calculation.

If users want to select the estimated atomic charge by ab initio calculation, users select this option. Also, users have to select the method, basis function and charge densith of method. ESP is the electrostatic potential fitting method. Mulliken is Mulliken density analysis.

Step5,Input the registrated e-mail address. After PolyParGen makes the moleculer parameter, the molecule’s parameter files are sent to the registrated e-mail address. Users have to input your e-mail.

Finaly, users push “Submit Molecule” button.

Make Molecule

This page shows How to meke molecules.

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)