Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Jul 3;45(W1):W331-W336.
doi: 10.1093/nar/gkx312.

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

Leela S Dodda  1 , Israel Cabeza de Vaca  1 , Julian Tirado-Rives  1 , William L Jorgensen  1
Affiliations

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

Leela S Dodda et al. Nucleic Acids Res. .

Abstract

The accurate calculation of protein/nucleic acid-ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the magnitude of the chemical space; the most critical issue is the estimation of a balanced set of atomic charges with the ability to reproduce experimental properties. The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for organic ligands, in the formats of commonly used molecular dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any phenomena based on intermolecular interactions with ligands via molecular mechanics simulations. It is free and open to all at jorgensenresearch.com/ligpargen, and has no login requirements.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
LigParGen Screenshots. Panel A, main input web page including a sample button and the Clustrmap tracking system. Panel B, ‘Draw Molecule’ input page screenshot including a sample molecule visualization. Panel C, output web page including a 2D representation and the JSMOL 3D visualizer. Panel D, LigParGen server main scheme.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Hospital A., Goni J.R., Orozco M., Gelpi J.L.. Molecular dynamics simulations: advances and applications. Adv. Appl. Bioinform. Chem. 2015; 8:37–47. - PMC - PubMed
    1. Sponer J., Banas P., Jurecka P., Zgarbova M., Kuhrova P., Havrila M., Krepl M., Stadlbauer P., Otyepka M.. Molecular dynamics simulations of nucleic acids. From tetranucleotides to the ribosome. J. Phys. Chem. Lett. 2014; 5:1771–1782. - PubMed
    1. Best R.B., Zhu, Shim X., Lopes J., Mittal P.E., Feig J., Mackerell M., MacKerell A.D. Jr. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and side-chain chi (1) and chi (2) dihedral angles. J. Chem. Theory Comput. 2012; 8:3257–3273. - PMC - PubMed
    1. Robertson M.J., Tirado-Rives J., Jorgensen W.L.. Improved peptide and protein torsional energetics with the OPLS-AA force field. J. Chem. Theory. Comput. 2015; 11:3499–3509. - PMC - PubMed
    1. Hornak V., Abel R., Okur A., Strockbine B., Roitberg A., Simmerling C.. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 2006; 65:712–725. - PMC - PubMed

Publication types