prime—Build and Refine Protein Structures

The prime program can be used to build initial (unrefined) protein models from an alignment to one or more templates, and to refine protein structures, using the Protein Local Optimization Program (PLOP). Structure refinement includes energy minimization, side-chain prediction, helix prediction, and loop prediction, with protocols for extended loop sampling, ultra-extended loop sampling, and cooperative loop pair sampling.

The command syntax is

$SCHRODINGER/prime [options] jobname

The input is read from the file jobname.inp and the structural output is written to the file jobname-out.maegz. If the input structure file for a job has alternate coordinates, a refinement is performed on the first set of alternate coordinates. When building models, you can specify multiple input files to build a multimer model. The file jobname.log contains text output, and jobname.err contains any error messages. The same syntax is used for restarting a failed job.

The -examples option displays a set of example input files, which are included in Examples of Prime Input Files.