FESetup: Automating Setup for Alchemical Free Energy Simulations

被引：85

作者：

Loeffler, Hannes H. ^{[1
]}

Michel, Julien ^{[2
]}

Woods, Christopher ^{[3
]}

机构：

[1] STFC Daresbury, Dept Comp Sci, Warrington WA4 4AD, Cheshire, England

[2] Univ Edinburgh, EaStCHEM Sch Chem, Edinburgh EH9 3JJ, Midlothian, Scotland

[3] Univ Bristol, BrisSynBio, Bristol BS8 1HH, Avon, England

来源：

JOURNAL OF CHEMICAL INFORMATION AND MODELING | 2015年 / 55卷 / 12期

基金：

英国生物技术与生命科学研究理事会; 英国工程与自然科学研究理事会;

关键词：

MOLECULAR-DYNAMICS; TOPOLOGY GENERATION; FORCE-FIELDS; GROMACS;

D O I：

10.1021/acs.jcim.5b00368

中图分类号：

R914 [药物化学];

学科分类号：

100701 ;

摘要：

FESetup is a new pipeline tool which can be used flexibly within larger workflows. The tool aims to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD. Post-processing methods like MM PBSA and LIE can be set up as well. Ligands are automatically parametrized with AM1-BCC, and atom mappings for a single topology description are computed with a maximum common substructure search (MCSS) algorithm. An abstract molecular dynamics (MD) engine can be used for equilibration prior to free energy setup or standalone. Currently, all modern AMBER force fields are supported. Ease of use, robustness of the code, and automation where it is feasible are the main development goals. The project follows an open development model, and we welcome contributions.

引用

页码：2485 / 2490

页数：6