Manually processing complex ligand structures.
The current version of H++ may not be able to process some complex ligand structures automatically.
To process such a structure "manually":
(a) edit a copy of the PDB file and delete the ligand atoms,
(b) process this PDB file through H++,
(c) edit "your_molecule.replaced.pqr" PQR file (from the results page)
and manually add back the ligand atoms with coordinates
from the original structure, along with their
charges (colums 57-62) and atomic radii (columns 66-70).
Make sure the atom labels in columns 1-6 are "ATOM ", and not "HETATM",
(d) process this updated PQR file through H++.
Some hints on how to obtain the charges and radii needed in teh step above
are decribed in the FAQ.
Here are examples of some PQR files for ligand complexes.
If your structure has one of these ligands, you may be able to use
the charges and atomic radii for the ligands from these files.
DO NOT use the atomic coordinates from these files since
they will be different for your structure. Instead, use the original coordinatesin your PDB file.
We will continue to expand this collection of examples with contributions from
our user community.
Sample ligand charges and atomic radii.
1. Heme group from myoglobin: heme.pqr
2. Retinal/Schiff base group from bacteriorhodopsin: retinal.pqr