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 
...