R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

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 embedd...

Full description

Saved in:
Bibliographic Details
Published in:Nucleic acids research 2011-07, Vol.39 (suppl_2), p.W511-W517
Main Authors: Vanquelef, Enguerran, Simon, Sabrina, Marquant, Gaelle, Garcia, Elodie, Klimerak, Geoffroy, Delepine, Jean Charles, Cieplak, Piotr, Dupradeau, François-Yves
Format: Article
Language:English
Subjects:
Calixarenes - chemistry
Internet
Molecular Dynamics Simulation
Quantum Theory
Software
Static Electricity
User-Computer Interface
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkr288