MacroModel Reference Manual - ISP

Chapter 1: Capabilities and New Features• Reads/writes old and new file formats. With Maestro, we introduce a new m2io file formatthat is self-defining and extensible. All programs are back-compatible with our oldmmio file format for both reading and writing; however, the new format has the ability tostore additional data, such as graphical representation of atoms between Maestro sessions(CPK, wireframe, etc.). Indeed, the m2io format can be used to store arbitrary data associatedwith molecules, atoms or bonds. Starting in MacroModel 8.0, Maestro format filesare written by default regardless of the format of the input structure file. However, youcan still direct MacroModel to write old MacroModel format files by specifying DEBG 6.• The TIME command reports CPU time(user+system) since the previous invocation ofTIME, or (on the first invocation) since program start.• The DEBG 1000 output of task timings is more detailed and informative.• Vectorized first derivative, second derivative, and energy calculating modules.• Network-distributed parallel processing for individual searches (MCMM, LMCS, LMC2, andmixed MCMM/LMCS and MCMM/LMC2).• Network-distributed parallel processing for serial calculations in which many input structuresare sequentially processed in similar ways. Two mechanisms are supported for performingthese calculations. One functions via commands such as NPRC placed in the .comfile; the other is a perl-based wrapper script for MacroModel called para_bmin. Bothmechanisms support distributed processing of serial searches (MCMM, LMCS, mixed MCMM/LMCS, SPMC, CGEN) and the former also supports multiple minimizations and MBAE calculations(minimizations and searches).• Compressed file format is supported for input and output Maestro files. Compression ofmulticonformer files greatly diminishes disk requirements.• RWND command allows the input or output file to be rewound and used as the input toanother procedure; only minimization is supported right now for the second procedure.We expect this to be most useful for reminimizing the output of a conformational search.• During a repetitive procedure, you can specify behavior if an iteration fails (BGIN).• The format of the .com file is checked when it is read in and warning messages are producedin the .log file for statements that are likely to be misinterpreted by MacroModeldue to formatting problems. If DEBG 960 is specified this reporting of format problems issuppressed. If DEBG 961 is specified then the job terminates immediately when such awarning is produced.• When solvation or force field parameters are missing for a structure in a serial calculationthe program continues with the next structure to be processed rather than stopping, unlessDEBG 49 is specified.8MacroModel 9.7 Reference Manual