title: R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.
abstract: 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.
authors: Laboratoire des Glucides, CNRS UMR 6219-UFR de Pharmacie, Université de Picardie-Jules Verne, 1, rue des Louvels, F-80037 Amiens cedex 1, France.
authors: Enguerran
authors: E
authors: Vanquelef
authors: Sabrina
authors: S
authors: Simon
authors: Gaelle
authors: G
authors: Marquant
authors: Elodie
authors: E
authors: Garcia
authors: Geoffroy
authors: G
authors: Klimerak
authors: Jean Charles
authors: JC
authors: Delepine
authors: Piotr
authors: P
authors: Cieplak
authors: François-Yves
authors: FY
authors: Dupradeau
references: J Chem Theory Comput. 2009;5(6):1680-1691
references: 20046995
references: J Comput Chem. 2004 Aug;25(11):1400-15
references: 15185334
references: J Phys Condens Matter. 2009 Aug 19;21(33):333102
references: 21828594
references: J Comput Chem. 2010 Mar;31(4):671-90
references: 19575467
references: J Comput Chem. 2007 Jan 30;28(2):495-507
references: 17186477
references: Theochem. 2000 Aug;527(1-3):149-156
references: 25309012
references: J Am Chem Soc. 1988 Mar 1;110(6):1657-66
references: 27557051
references: J Comput Chem. 2002 Dec;23(16):1623-41
references: 12395429
references: Biopolymers. 2000-2001;56(4):257-65
references: 11754339
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D360-7
references: 17962302
references: Proteins. 2006 Nov 15;65(3):712-25
references: 16981200
references: Biopolymers. 2000-2001;56(4):232-56
references: 11754338
references: J Comput Chem. 2008 Mar;29(4):622-55
references: 17849372
references: Phys Chem Chem Phys. 2010 Jul 28;12(28):7821-39
references: 20574571
references: J Comput Chem. 2005 Dec;26(16):1668-88
references: 16200636
references: J Comput Chem. 2004 Jul 15;25(9):1157-74
references: 15116359
references: Adv Protein Chem. 2003;66:27-85
references: 14631816
references: J Am Chem Soc. 1974 Aug 21;96(17):5319-27
references: 4851860