mol

This option gives the initial molecular coordinates.

• Explicit XYZ Coordinates
• XYZ File Name
• PDB File Name

Explicit XYZ Coordinates

You can simply give XYZ coordinates in Angstrom:

mol
  O   0.00000000000000      0.05011194954430      0.05011194954224
  H   0.00000000000000     -0.06080277603381      1.01069082652926
  H   0.00000000000000      1.01069082648951     -0.06080277607149
end

XYZ File Name

You can give the XYZ file name (path can be included if necessary)

mol
  ../mols/water.xyz
end

PDB File Name

You can give the PDB file name (path can be included if necessary)

mol
  proteins/ala3.pdb
end