Gaussian: Tutorial on Converting Brookhaven Protein Data Bank (PDB) Files to Gaussian Input Files

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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