The pl_analysis Stage

Overview
Default Configuration

This stage performs an analysis of protein and ligand interactions. There are two keywords, ligand_asl and protein_asl, which specify the ASL expression for the ligand and protein, respectively. If not specified, the stage tries to automatically detect the appropriate values. If “none” is specified, the class ignores analysis for that parameter. Note that, if applicable, this stage only runs on the last replica of the relevant simulation.

The interactions can be graphically explored in the Simulation Interactions Diagram Panel.

Table 1. Keywords for the pl_analysis stage
Keyword	Description
`ligand_asl`	ASL expression of the ligand used for analysis.
`protein_asl`	ASL expression of the protein used for analysis.

Default configurations for the pl_analysis stage. A {type} value is shown for keywords which do not have defaults set. See General multisim Stage Keywords for descriptions of general keywords

{
   compress = "$MAINJOBNAME_$STAGENO-out.tgz"
   dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MAINJOBNAME_$STAGENO"
   dryrun = false
   effect_if = {list}
   jlaunch_opt = []
   jobname = "$MAINJOBNAME_$STAGENO"
   ligand_asl = ""
   prefix = ""
   protein_asl = ""
   should_skip = false
   should_sync = true
   struct_output = ""
   title = {str}
   transfer_asap = false
}