prime_mmgbsa—Calculate Ligand Binding Energies

You can run Prime MM-GBSA from the command line with the input file written from the panel. The syntax is as follows:

$SCHRODINGER/prime_mmgbsa [options] input-file

The input file must be a Maestro file. By default, the receptor must be the first entry, followed by one or more ligands (i.e. Glide pose viewer file format). The file can be compressed (.mae.gz, .maegz) or uncompressed (.mae). If the -ligand option is specified, the file must contain ligand-receptor complexes.

To restart a failed job, run it again with the -RESTART option.

If you have a command input file, jobname.inp, as written from the panel, for example, you can replace the input structure file and the command options with this file. The command input file contains a keyword for the structure input, so it need not be specified. You can also specify command options as well as a command input file, to override values specified in the file.

The standard Job Control options are accepted—see Running Jobs From the Command Line—except that -HOST and -SUBHOST are used for distributing jobs, not -DRIVERHOST. For a description of the program options, run the command with the -h option.