NWChem/contrib/pdb_tools

Tools to manipulate PDB files

General PDB files need tools to apply transformations to them. As this need is quite common there a number of tools out there already and where applicable you should use them. Examples of such tools are:

• convpdb.pl
• pdb4amber
• charmmlipid2amber.py
• pdbfixer

Unfortunately some of these tools try to be too helpful. For example convpdb.pl will not only scale the coordinates in a PDB file if you ask for it, but it will also drop all TER records, rename HOH to TIP3, drop the CRYST1 record, and drop the chemical symbol at the end of the line. This might leave you with a useless result.

The tools in this directory do exactly what it says on the tin, nothing less and nothing more. The tools provided here are:

• pdb_amber2nwchem
  • Convert an Amber PDB file into an NWChem PDB file by renaming atoms and residues.
• pdb_large
  • Interconvert a PDB file between the regular PDB file format and the NWChem PDB file format for large molecular systems. In essence the large PDB format allows 6 digits for the residue number instead of 4.
• pdb_scale.F
  • Scale the atomic coordinates and the box size with a specified factor.
• pdb_supercell.py
  • Build a supercell of a given PDB file by doubling the initial molecular system in the requested direction.