MODEL COMMANDS

Model commands are used for managing model files, including read, write, and modification, which are used in all programs except DFFLSV.

OPEN (A)

$MODEL=$OPEN
  <filepath 1>
  <filepath 2>
  ...
$End

This is an array command loads multiple models. Each line is a model file in format of msd, pdb or mol2.

SAVE (A)

$MODEL=$SAVE
  <filename 1>
  <filename 2>
  ...
$END

A command saves models in MSD format. The order of files must be the same as loaded. The filenames can be different from the input.

SAVEALL (S)

$MODEL=$SAVEALL

This command saves all models to MSD files. The filenames are the same as loaded. Note that if the loaded files are in MSD format, they will be overwritten.

CLOSE (S)

$MODEL=$CLOSE

Command closes all opened models, any changes made to the models will be lost unless saved.

SETTYPE (D)

$MODEL=$SETTYPE
  RULER=<typing rule>
$END

This command assigns atom types to opened models using a specified typing rule. The typing rule can be any typing script (such as TEAM.ext) save in the /typingScripts folder or "DEFAULT".

SETFC (D)

$MODEL=$SETFC
	REMOVE = FALSE|TRUE
	OVERWRITE = TRUE|FALSE
$END   

Sets the formal charges, two parameters are accepted: REMOVE and OVERWRITE. REMOVE will set all atoms to zero formal charges. This command will supersede other options. OVERWRITE is used to treat existing values. If TRUE, all existing values will be erased and then recalculated. If FALSE, the existing values will not be changed, only atoms without formal charges will be calculated. The default is TRUE.

GUESSBOND (S)

$MODEL=$GUESSBOND

A simple command that build connectivity and then calculate bond orders. The existing connectivity will be erased and recalculated using the atom-atom distances.

GUESSBONDORDER (S)

$MODEL=$GUESSBONDORDER

command calculates the bond orders, the existing connectivity is kept.