A World Wide Web-service to aid the development of AMBER parameters using analogy to standard parameters

Abstract

A World-Wide Web service has been constructed to assist the development of force field parameters extending the AMBER force fields. This service extracts parameters from the standard AMBER force field parameter databases. From a Web-based interface the user can choose between bond, angle and torsional parameters with certain constraints on element and/or atom hybridization. The software constructed for the purpose of finding appropriate parameters will locate standard AMBER force field parameters matching the user specification. For bond and angle parameters a scatter plot of the reference values against force constants is provided. This service has been produced to assist in extraction and evaluation of parameters that may be useful for molecules other than proteins and nucleic acids.