Laboratoire des Glucides, CNRS UMR 6219-UFR de Pharmacie, Université de Picardie-Jules Verne, 1, rue des Louvels, F-80037 Amiens cedex 1, France.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W511-7. doi: 10.1093/nar/gkr288. Epub 2011 May 23.
R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.
RED Server 是一个独特的、开放的网络服务，旨在推导非极化 RESP 和 ESP 电荷，并为新的分子/分子片段构建力场库。它为计算生物学家提供了一种方法，可以从力场库中推导出严格基于分子静电势的电荷，这些电荷已经准备好用于力场开发、电荷验证和分子动力学模拟。RED Server 接口量子力学程序、RESP 程序和最新版本的 RED 工具。已经开发了一种两步方法。第一步是准备 P2N 文件，以严格定义构建力场库时所需的关键元素，如原子名称、拓扑和化学等效性。然后，使用 P2N 文件从 Tripos mol2 格式的力场库中推导出嵌入的 RESP 或 ESP 电荷。在复杂情况下，会生成一整套力场库或力场拓扑数据库。RED Server 中开发的其他功能包括帮助服务、演示、教程、常见问题解答、基于 Jmol 的工具，这些工具可用于构建 PDB 输入文件并解析 RED Server 输出，以及一个图形排队系统，允许任何用户检查 RED Server 作业的状态。
