Combine component PDBs
As noted earlier BAC expects the PDB to have a set structure - protein, ligand and then solvent.
It also expects TER cards between chains.
During this tutorial we have prepared files for each of these sections, edited to meet the requirements of Amber and BAC:
- Protein: 4bjx-protein-stripped.pdb
- Ligand: l01.pdb
- Solvent: 4bjx-solvent.pdb
If all three files have been properly prepared the combination of the sections can be as simple as:
cat 4bjx-protein-stripped.pdb l01.pdb 4bjx-solvent.pdb > bet-l01.pdb
When naming the final PDB it is helpful to use a meaningful name. Here bet-l01.pdb combines the protein name (it is a BRD4 structure, these are members of the Bromo-and Extra-Terminal domain, BET, family) and the ligand name.
Check this PDB to ensure that there is a line containing only the text TER between the protein, ligand and solvent sections of the file.
Be careful to ensure that any END cards only appear as the very last line of the file (hint: you need to change an END into a TER in the file as generated above).
Add header
Additionally, a BAC specific header should be included at the top of the file. This simply contains the number of protein chains included.
REMARK 6 PROTEIN CHAINS 1
As the PDB format is based on columns the REMARK 6 PROTEIN CHAINS section (up to the figure for the number of protein chains) must be reproduced exactly.
The protein used here contains only one chain, so edit bet-l01.pdb file accordingly. An example PDB file can be dowloaded from here.
Organize files and create tarball
For upload into BAC a particular arrangement of files is needed.
Create a directory, named using the lowercase version of the ligand residue name:
mkdir l01
Copy the .frcmod and prep files into this directory.
cp l01.frcmod l01
cp l01.prep l01
Finally, create a tarball containing the directory we created:
tar cfv bet-l01.tar l01
An example tarball can be downloaded here. The two inputs needed for use in the ufBAC are thus the full system PDB (bet-l01.pdb) and this tarball of the ligand parameterization (bet-l01.tar).
In the next section we detail the use of scripts to check that the inputs created are ready for successful use in BAC.