README.md
1Tools to manipulate PDB files
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3
4General PDB files need tools to apply transformations to them. As this need is
5quite common there a number of tools out there already and where applicable
6you should use them. Examples of such tools are:
7
8* convpdb.pl
9* pdb4amber
10* charmmlipid2amber.py
11* pdbfixer
12
13Unfortunately some of these tools try to be too helpful. For example `convpdb.pl`
14will not only scale the coordinates in a PDB file if you ask for it, but it will
15also drop all TER records, rename HOH to TIP3, drop the CRYST1 record, and drop
16the chemical symbol at the end of the line. This might leave you with a useless
17result.
18
19The tools in this directory do exactly what it says on the tin, nothing less
20and nothing more. The tools provided here are:
21
22* pdb_amber2nwchem
23 * Convert an Amber PDB file into an NWChem PDB file by renaming atoms and
24 residues.
25* pdb_large
26 * Interconvert a PDB file between the regular PDB file format and the
27 NWChem PDB file format for large molecular systems. In essence the
28 large PDB format allows 6 digits for the residue number instead of 4.
29* pdb_scale.F
30 * Scale the atomic coordinates and the box size with a specified factor.
31* pdb_supercell.py
32 * Build a supercell of a given PDB file by doubling the initial molecular
33 system in the requested direction.
34