MacroModel Reference Manual - ISP

MacroModel Reference ManualAppendix EAppendix E: The BMFF ProtocolE.1 PurposeBMFF (BatchMin Force Field) is an interprocess communication protocol which allowsMacroModel to obtain force-field interactions from an external process. In this context, Macro-Model is the client and the external process is the server.The purpose of this appendix is to provide a functional description of the protocol, rather thanto define the underlying implementation details. The current implementation is based on pipes.There is no requirement at present that the server be re-entrant; that is, at present, each clientprocess starts up and terminates its own server process.In the current implementation, the named pipes for communication between MacroModel andthe server process are set up in:• The directory named in the environment variable FIFO_LOCATION, if this variable exists;• Otherwise, /tmp, if this directory exists;• Otherwise, the local directory.Note: On SGI systems, named pipes are very slow on NFS-mounted filesystems. Use anexplicit FIFO_LOCATION in the environment if the above hierarchy does not result inthe use of a locally mounted disk for the location of the named pipes.E.2 OverviewThe MacroModel force field continues to be specified by means of the FFLD command in thecommand file. In the past (i.e., prior to the implementation of BMFF), the first argument of thiscommand was limited to the values 1 through 5; for example, the value 3 specifies the AMBERforce field.BMFF extends this mechanism as follows. If the first argument to the FFLD command is 10, anexternal process is started to generate force-field interactions. MacroModel obtains informationit needs to initiate, control, and utilize the results of this process from an extended forcefieldfile called fnn.fld, where nn is the value of this argument.Values between 10 and 99, inclusive, are reserved for assignment by the MacroModel developmentteam; for example, the value 10 is assigned to the MMFF force-field. Then the MMFFMacroModel 9.7 Reference Manual 221