Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
Nucleic Acids Res. 2017 Jul 3;45(W1):W331-W336. doi: 10.1093/nar/gkx312.
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.
通过基于力场的方法准确计算蛋白质/核酸-配体相互作用或凝聚相性质，需要精确描述分子间相互作用的能量。尽管在力场方面取得了进展，但由于化学空间的巨大，小分子参数化仍然是一个未解决的问题；最关键的问题是估计具有能够重现实验性质的平衡原子电荷集。LigParGen 网络服务器为生成有机配体的 OPLS-AA/1.14*CM1A(-LBCC)力场参数提供了直观的界面，支持常用的分子动力学和蒙特卡罗模拟包的格式。对于有兴趣通过分子力学模拟研究任何基于与配体相互作用的现象的研究人员来说，这个服务器具有很高的价值。它是免费的，开放给所有人，网址是 jorgensenresearch.com/ligpargen，无需登录。
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