SOLVENT

 NAME
SOLVENT – Reset to zero the position of the center of mass of the solvent atoms.

 SYNOPSIS
SOLVENT [ON] SOLVENT [OFF]

 DESCRIPTION
If ON is specified, ORAC assumes that a solvent is present and its coordinates are read in from the file PDB specified by the directive READ_PDB in this environment. This command is not mandatory as, if the solvent is present the environment &SOLVENT (which has the same effect of SOLVENT [ON] must be entered anyway in order to specify how to generate the solvent or the number of solvent molecules in the PDB file. When SOLVENT OFF is specified, the namelist &SOLVENT must be omitted.

 EXAMPLES

 
&SETUP
  READ_PDB solvent.pdb
  SOLVENT ON
&END   
...
&SOLVENT
  ADD_UNITS 432
&END
...
&PARAMETERS
  ...
  JOIN SOLVENT
     hoh
  END
&END 
...

A solvent (432 molecules) is present and the coordinates are read in from the file PDB. The “residue” sequence for the solvent found in the PDB must match that given in the JOIN SOLVENT (&PARAMETERS) directive. If a solute is also present and its coordinates are given in the PDB file specified by the READ_PDB command, then the coordinates of the solvent molecules must follow those of the solute in the PDB file. An example is the following

&SETUP
  READ_PDB solute+solvent.pdb
  SOLVENT ON
  SOLUTE ON 
&END   
...
&SOLVENT
  ADD_UNITS 432
&END
...
&PARAMETERS
  ...
  JOIN SOLVENT
     hoh
  END
  JOIN SOLUTE
    ala-h ala ala ala-o
  END
&END 
...