The R.ED. tools: advances in RESP and ESP charge derivation and force field library building

被引:768
作者
Dupradeau, Francois-Yves [1 ,2 ]
Pigache, Adrien [1 ,2 ]
Zaffran, Thomas [1 ,2 ]
Savineau, Corentin [1 ,2 ]
Lelong, Rodolphe [1 ,2 ]
Grivel, Nicolas [1 ,2 ]
Lelong, Dimitri [1 ,2 ]
Rosanski, Wilfried [1 ,2 ]
Cieplak, Piotr [3 ]
机构
[1] Univ Picardie Jules Verne, CNRS, UMR 6219, F-80037 Amiens 1, France
[2] Univ Picardie Jules Verne, UFR Pharm, F-80037 Amiens 1, France
[3] Sanford Burnham Inst Med Res, La Jolla, CA 92037 USA
基金
美国国家卫生研究院;
关键词
POTENTIAL DERIVED CHARGES; MOLECULAR-ORBITAL METHODS; NET ATOMIC CHARGES; N-METHYL-ACETAMIDE; ELECTROSTATIC POTENTIALS; CONFORMATIONAL ENERGIES; COMPUTATIONAL CHEMISTRY; EFFICIENT GENERATION; GAUSSIAN EXPANSIONS; DIMETHYL-SULFOXIDE;
D O I
10.1039/c0cp00111b
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
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 de. ning 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 de. ning 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.
引用
收藏
页码:7821 / 7839
页数:19
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