Place Cu(I) or Cu(II) into histidine coordination sites in a PDB file. Cu position is estimated geometrically — structure optimisation should be performed after placement before any MD or QM/MM use.
numpy scipy
python3 CuBind_F.py protein.pdb -1 # Cu(I) · 2×His
python3 CuBind_F.py protein.pdb -2 # Cu(II) · 3×HisOutput: <stem>_1Cu.pdb / <stem>_2Cu.pdb
| Flag | Default | Description |
|---|---|---|
--cu-n-ideal |
2.00 Å | Target Cu–N bond length |
--cu-n-max |
2.60 Å | Max accepted Cu–N distance |
--don-cutoff |
7.00 Å | Max donor–donor distance |
--cu-sep |
5.00 Å | Min Cu–Cu separation |
--clash |
1.80 Å | Min Cu–heavy atom distance |
- Cu only — no Zn, Fe, or other metals
- His-N donors only — HIE→ND1, HID→NE2; HIP skipped
- Cu position is a geometric estimate; run energy minimisation before downstream use
- No water or non-His ligands considered
This project is distributed under the MIT License.