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. 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.

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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

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