Running a Semiempirical Module Job from the Command Line

To run a semiempirical job from the command line, use the following syntax:

$SCHRODINGER/run semi_emp.py [options] [job-options] structure-files

Each input structure file can contain multiple structures.The files can be in Maestro, SD, MOL2, or MOPAC format. All the input structure files must be of the same type, (e.g. all .mae). For a description of the command options, run the command with the -h option, or see semi_emp.py Command Help.

If you use a MOPAC file (.mop) as input, the job is run with this file and a MOPAC .out file is returned, but no Maestro file is returned. That is, the job is handled as if you ran the MOPAC executable directly. The same is true if you use multiple MOPAC files as input.

If you use a Maestro, SD, or MOL2 file as input, a single Maestro file is returned with the results, and the MOPAC results are returned in a single output file (.out).

If you provide multiple input files, you can run the job in parallel, with a subjob for each input file. You can do this by setting the number of processors to the number of input files with the -HOST option. If you have fewer processors, the files are distributed over the processors, and run serially on each processor. A single Maestro file is returned with all the results if structure input files were provided, in addition to the files from the individual subjobs.

As an example of a single input file, if you have a Maestro file called myfile.mae that contains three ligands whose geometries you would like to optimize with the PM3 method, and you want to print out the final bond order matrix, and the sigma-pi bond order matrix, you would use this command:

$SCHRODINGER/run semi_emp.py -method pm3 -keywords "bonds pi" myfile.mae

This job produces an output file named myfile.out, together with an output structure file called myfile_out.mae, which contains the final geometries, the method used, the semiempirical energy, and the atomic charges (which are calculated by default). This structure file may be manually imported into Maestro. Atoms may be labeled with their partial charges by selecting Atomic Charge from the list of available labels in the Atom Labels panel. These charges may also be used in docking calculations with Glide. In addition, a log file is produced, which includes information about the job options used.