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

被引：1060

作者：

Dodda, Leela S. ^{[1
]}

de Vaca, Israel Cabeza ^{[1
]}

Tirado-Rives, Julian ^{[1
]}

Jorgensen, William L. ^{[1
]}

机构：

[1] Yale Univ, Dept Chem, 225 Prospect St, New Haven, CT 06520 USA

来源：

NUCLEIC ACIDS RESEARCH | 2017年 / 45卷 / W1期

基金：

美国国家卫生研究院;

关键词：

SOLVATION FREE-ENERGIES; FORCE-FIELD; POTENTIAL FUNCTIONS; MOLECULAR-DYNAMICS; PARTIAL CHARGES; ATOMIC CHARGES; CHARMM; SIMULATION; MODEL; ENERGETICS;

D O I：

10.1093/nar/gkx312

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：W331 / W336

页数：6

共 42 条

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