AMBER/CHIMERA INTEGRATION

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. It is typically an arduous process to learn how to properly prepare input files for molecular mechanics programs. Amber is no different from other MM programs in this regard. The aim of this project is to greatly reduce the effort required to prepare input for the Amber suite of programs and in some cases to make it possible to directly execute those programs/functions from within Chimera and view the output thereof as appropriate. Wei Zhang is the principal developer of sleap, a new program for creating and editing molecular systems for Amber. He is coordinating closely with Eric Pettersen of the Chimera development team in creating interfaces from Chimera into sleap's functionality. Dr. Zhang has direct commit access into Chimera's SVN source code repository, and changes he makes appear in the next Chimera daily build, which allows for quick turnaround for testing and debugging.