The assign_custom_charge Stage

Overview
Default Configuration

This stage enables custom charge assignment for the ligand structures in the input file.

Ligands must be in separate structures, otherwise custom charges are not assigned. All other structures are passed through the stage unchanged. In a workflow that also assigns a forcefield, assign_custom_charge must be called prior to assign_forcefield.

Table 1. Keywords for the assign_custom_charge stage
Keyword	Description
`mode`	One of: `keep`, `clear`, `assign`. `keep` (default) preserves the custom charges already assigned to the structures, but does not assign new ones. `clear` removes any existing custom charges. `assign` clears existing custom charges, and newly assigns custom charges to the structures.
`canonicalize_inp_conformation`	Whether the input structure should be canonicalized before custom charge assignment. Custom charge assignment of unrelaxed structures may be sensitive to the structures conformation; canonicalizing the input before assignment may lead to more consistent simulation results. This is done by default for FEP+ Solubility hydration-only jobs.

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

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