Losing Zinc metal in Macromolecule when converting to PDBQT

[Niek]

I am trying to solve a similar problem, but this time with a metal (Fe) in the ligand instead of in the macromolecule. I have tried changing HETATM to ATOM (as suggested above), but that didn't help. Because the ligand does not include a definition of "chains", I can't really put the metal into the chain. The odd thing is that if I use K (which is not supported if I understand things right), this atom type is included correctly and I can dock without problems. Is there a generally working solution for keeping metals when going PDB -> PDBQT?

[sargis]

I am trying to solve a similar problem, but this time with a metal (Fe) in the ligand instead of in the macromolecule. I have tried changing HETATM to ATOM (as suggested above), but that didn't help. Because the ligand does not include a definition of "chains", I can't really put the metal into the chain. The odd thing is that if I use K (which is not supported if I understand things right), this atom type is included correctly and I can dock without problems. Is there a generally working solution for keeping metals when going PDB -> PDBQT?

Could you please attach a sample ligand file so that we can reproduce this? I just tried the following compound from PubChem and it worked fine for me:
http://pubchem.ncbi.nlm.nih.gov/summary ... cid=115140

I did OpenBable energy minimization, since PubChem didn't have 3D SDF for this molecule. As you can see in the attached PDBQT, it kept the metal (Fe) and autogrid did generate Fe.map files for this.

[sagarriya]

you people are editing charge by opening the pdbqt file from plain note pad or Word, isn't it? I did same for my ligand 1C3S but it said "charges are not intregal, correct "this" residues by "this" value" . Now what to do? Which atom of that residue to correct by this value? I changed every atom of that residue but then it again said some other ligand had causing non integral charges. why isn't there a detailed tutorial about charge correction in receptor?