MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg3 Atom 3If arg1, arg2, and arg3 are nonzero and arg4 is zero, GEOM prints the angle betweenthe atoms specified in arg1, arg2, and arg3. If arg5 is nonzero, it is ignored.arg4 Atom 4If arg1, arg2, arg3, and arg4 are nonzero, GEOM prints the dihedral angle between theatoms specified in arg1, arg2, arg3, and arg4. If arg5 is nonzero, it is ignored.arg5Spin-spin coupling constantIf arg5 > 0, GEOM prints the spin-spin coupling constant J between the atoms specifiedin arg1 and arg2, subject to the following conditions:• The atoms given by arg1 and arg2 are hydrogen atoms• The hydrogen atoms are connected through two carbon atoms• The values of arg3 and arg4 are zero.If either of the first two conditions is not met, a warning is printed and the calculationcontinues without calculating the coupling constant.TIME — report cpu TIME (user+system)The TIME command reports CPU time (user+system) since the previous invocation of TIME, or(on the first invocation) since program start. See also DEBG 1000 for more detailed and informativeoutput on task timings.JWRT — Journal WRiTeThe JRED and JWRT commands are provided in order to use MacroModel as a force-fieldserver in connection with procedures being carried out by other processes. JWRT writes out auser-specifiable combination of coordinates, energy, gradient, and Hessian in binary form thatthe co-process can read. JRED reads in coordinates in a similar format that have been writtenout by the co-process. Thus, the co-process can provide coordinates to MacroModel, instruct itto compute the energetic terms, read back those energetic terms, manipulate the molecule, andcomplete the cycle. The way this facility is provided now, MacroModel has to be launchedanew for each new calculation (for example, by a system() call from the client process);however, we may later enhance this facility to make it more fully interactive.arg1Write coordinatesIf arg1 is nonzero, write out the coordinates.150MacroModel 9.7 Reference Manual