The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.
The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.
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DOI：
10.1039/c0cp00111b
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发表时间：
2010-07-28
期刊：
影响因子：
--
通讯作者：
Cieplak P
中科院分区：
文献类型：
--
作者：
Dupradeau FY;Pigache A;Zaffran T;Savineau C;Lelong R;Grivel N;Lelong D;Rosanski W;Cieplak P
推导原子电荷和为新分子构建力场库是开发使用分子力学进行结构和基于能量的分析所需的力场时的关键步骤。推导一组残基的流行RESP电荷是一个复杂且容易出错的过程，因为它取决于许多输入参数。为了解决这些问题，R.E.D.已经开发了工具（RESP和ESP电荷导出，http：//q4md-forcefieldtools.org/RED/），以自动和直接的方式执行电荷导出。R.E. D程序处理元素周期表中直到溴的化学元素。它接口不同的量子力学程序用于几何优化和计算分子静电势（S），并使用RESP程序进行电荷拟合。通过定义严格的优化标准，并通过控制每个优化的几何结构的分子取向，电荷值在任何计算机平台上以0.0001 e的精度再现。电荷可以使用多种构象进行拟合，使其适合于分子动力学模拟。研发还允许在多分子电荷拟合期间定义电荷约束，其用于导出分子片段的电荷。最后，R.E.D.将电荷合并到力场库中，易于在分子动力学计算机包中使用。对于复杂的情况，例如属于共同家族的一组同源分子，生成整个力场拓扑数据库。目前，原子电荷和力场库已经开发了五十多个模型系统，并存储在RESP ESP电荷DDataBase。选定的结果有关的非极化电荷模型的介绍和讨论。
Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure, because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, http://q4md-forcefieldtools.org/RED/) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.
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影响因子：
6.1
作者：
CONNOLLY, ML
通讯作者：
CONNOLLY, ML
DOI：
10.1088/0953-8984/21/33/333102
发表时间：
2009-08-19
期刊：
Journal of physics. Condensed matter : an Institute of Physics journal
影响因子：
--
作者：
Cieplak P;Dupradeau FY;Duan Y;Wang J
通讯作者：
Wang J
影响因子：
3
作者：
COX, SR;WILLIAMS, DE
通讯作者：
WILLIAMS, DE
影响因子：
3
作者：
CHIRLIAN, LE;FRANCL, MM
通讯作者：
FRANCL, MM
影响因子：
3
作者：
Duan, Y;Wu, C;Kollman, P
通讯作者：
Kollman, P