The extract_structures Stage

System Preparation
Structure Modification
  • Overview
  • Default Configuration

This stage extracts one or more structures from an input .mae file, clears any previously applied restraints, and deletes any duplicated structure properties. The stage is used as a part of structure preparation for FEP+ calculations.

Table 1. Keywords for the extract_structures stage

Keyword

Description

start_index

Starting index (inclusive) to use for extraction. Used on the structure from the preceding stage.

end_index

Ending index (exclusive) to use for extraction. Used on the structure from the preceding stage.

keep

List of structure tags used to identify the structures to extract. This is used instead of a start and end index. Elements of the list can include: ligand, receptor, membrane, solvent, complex, fragment.

Default configurations for the extract_structures 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}
   end_index = {int}
   jlaunch_opt = []
   jobname = "$MAINJOBNAME_$STAGENO"
   keep = {list}
   prefix = ""
   should_skip = false
   should_sync = true
   start_index = {int}
   struct_output = ""
   title = {str}
   transfer_asap = false
}