If a molecular structure is described in Brookhaven Protein Data Bank (PDB) file format, it can be converted to Gaussian input file using the NewZmat command. For example, one can obtain a PDB file for water ( water.pdb ) which has the following listing:

HEADER
REMARK WATER MOLECULE H2O
HETATM    1  H   UNK  0001      0.000   0.780   0.190
HETATM    2  O   UNK  0001      0.000   0.000  -0.380
HETATM    3  H   UNK  0001      0.000  -0.780   0.190
CONECT    1    2
CONECT    2    1   3
CONECT    3    2
END

Type the following command at the prompt and a Gaussian input file for water ( water.com ) will be generated:

newzmat -ipdb water.pdb water.com

NewZmat will ask for charge and spin multiplicity of the molecule. For water, there is no charge and spin multiplicity is 1, so hitting return will take the default.

Charge and Multiplicity [0,1]?

The Gaussian input file ( water.com) for water is then generated. By default, the file is set up to perform the Hartree-Fock calculation using the 6-31G basis set. The water molecule is described in Z-matrix format. Here is the listing of the water.com file:

# HF/6-31G* Test

WATER MOLECULE H2O
   0   1
 O
 H,1,R2
 H,1,R2,2,A3
      Variables:
 R2=0.96607453
 A3=107.68362912

This file can be modified to perform different kinds of calculations. Also, the title line can be changed. For example, if we want to perform geometry optimization for water molecule using the Hartree-Fock calculation with a 6-31G basis set, the file water.com can be changed to the following:

# HF/6-31G* Opt Test
H2O Hartree Fock Geometry Optimization with 6-31G Basis Set
   0   1
 O
 H,1,R2
 H,1,R2,2,A3
      Variables:
 R2=0.96607453
 A3=107.68362912

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