Protein tools

MOPAC contains several features designed specifically for proteins. As suggested by its name, the MOZYME solver was designed to study proton transfer reactions in enzymes. An atomistic study of proteins such as enzymes needs to start with atomistic structure, which can be large and complicated. A popular source of protein structure data is the Protein Data Bank (PDB), and MOPAC has tools for processing data from this source and preparing it for MOZYME calculations. These tools are associated with specific MOPAC keywords, and the simplest of these tools/keywords are summarized below. See the online MOPAC manual for more detailed information on advanced protein functionality such as transition state searches for enzymatic reactions and some worked examples.

GEO_DAT #

MOPAC can read protein structures that are stored in the PDB file format, usually with a .pdb file extension. Specifically, a PDB file protein.pdb file can be read by using the GEO_DAT="protein.pdb" keyword instead of inputting the protein structure directly into a MOPAC input file. In addition to the structure data, MOPAC retains the atom labels from the PDB file.

In recent years, the PDB has switched from the PDB file format to the mmCIF file format with a .mmcif file extension, but MOPAC presently does not directly support the mmCIF file format.

PDBOUT #

This keyword causes MOPAC to print the output structure of a calculation in the PDB file format. As with other output files, the .pdb file extension is appended to the name of the input file. Take care not to overwrite existing .pdb files unintentionally.

RAMA #

This keyword causes MOPAC to print the Ramachandra angles (phi, psi, and omega) for the residues of a protein in the .out output file.

RESIDUES #

This keyword causes MOPAC to relabel the atoms in a protein with a unique atom label for each atom in an amino acid residue, a 3-letter abbreviation for the residue, a letter for the polypeptide chain, and a number for the position in the polypeptide.

RESEQ #

This keyword causes MOPAC to reorder the atoms in a protein into a standard PDB file sequence.

ADD-H #

This keyword causes MOPAC to remove all of the hydrogen atoms from a structure and add new hydrogen atoms to create chemically sensible closed-shell organic molecules. Because hydrogen positions in proteins cannot be reliably identified by x-ray crystallography, PDB files often have missing or omitted hydrogen atoms. There is some unavoidable ambiguity in the assignment of hydrogen atoms, and the ADD-H feature was designed and tested with the sensible hydrogenation of proteins in mind.

SITE #

This keyword can be used to adjust the behavior of the ADD-H keyword. The simplest use of this keyword is SITE=(SALT), which forces all terminal nitrogen atoms within 4 Angstroms of a caboxylic acid group to become a salt bridge. This causes the hydrogen and charge assigment of (NH3)+ and (COO)- instead of (NH2) and (COOH). See the online MOPAC manual for a complete explanation of this keyword.