LICHEM converts a TINKER XYZ file to a standard XYZ file. That means that a
PDB file would first need to be converted to a TINKER XYZ, which can be done
using pdbxyz.
pdbxyz is a program in the TINKER software package. Its usage is:
$ pdbxyz name_of_pdb.pdb -key tinker.key
Running this command with a complete PDB often causes issues. One way to avoid these issues is to break up the PDB into several smaller PDBs and convert them individually. This is particularly critical for double-stranded nucleic acids, where each strand needs to be in its own PDB file to convert correctly. It is recommended that every location that a TER would be starts a new file to convert, as well as adding in other new files. So, one system could be broken into:
- Protein
- Non-standard residue
- Substrate nucleic acid strand
- Complement nucleic acid strand
- Metal
- Counterions
- Water
After using pdbxyz on each of these individual files, all the files can be
combined into a single TINKER XYZ file using TINKER’s xyzedit.
$ xyzedit name_of_protein.xyz -key tinker.key
This will bring up a list of options, one of which is
Append a second XYZ file to current one.
Enter the number corresponding to this option (likely 18) and then enter in
the next XYZ file in the order you’d like them to be appended.
Once you’ve finished choosing this option and file addition process, hit enter
without entering a new option.
The new, combined file will be named name_of_protein.xyz_2.