VORONOI

NAME
VORONOI - Compute the Voronoi polihedra of atoms, residues and molecules

SYNOPSIS

VORONOI
    ...
    ...
END

DESCRIPTION
The command VORONOI opens an environment which includes a series of subcommands which allow to compute average and instantaneous properties related to the Voronoi polihedra of the solute and of the solvent.

compute accessibility
Compute the area of the Voronoi polihedron for all residues of the solute (computed as the sum of the voronoi volumes of the individual atoms) and evaluate for each residue the fraction of the surface that is accessible to the solvent (solute and solvent as defined in the command JOIN(&PARAMETERS))

compute contact_solute  int1  int2
Compute the contact surface among selected solute residues with residue numer int1 and int2 as in the the PDB file.

compute neighbors
Compute the Voronoi coordination number relative to the whole solute-solute, solvent-solvent and solute-solvent contacts.

compute volume
Compute the Voronoi volumes of all residues in the solute.

cutoff value
values the cutoff (Å) for

heavy_atoms
Use only non hydrogen atoms for evaluating Voronoi polihedra

print nprint   OPEN  filename
Print all output as to file filename every nprint configurations

EXAMPLES

VORONOI
  print 5 OPEN 6.vor
  cutoff 8.0 
  heavy_atoms 
  compute contact_solute 1 2
  compute contact_solute 5 6
  compute volume
  compute neighbors
  compute accessibility 
END

In this example we compute the voronoi volumes, areas and accessibility and neighbors for the residues of a proteins every 5 configurations. Also the contact surfaces between residues 1 and 2 and residue 5 and 6 are evaluated. All output are printed to the file 6.vor.

WARNINGS
VORONOI commands works only in conjunction with the &ANALYSIS environment. Experimental - Unsupported