Good evening,
I have been trying to input a PDB file onto HADDOCK but everytime I try to submit the file comes up with an error. I have been able to fix multiple errors using PyMOL but now it says that the PBS contains an elemental ion CA without specified charge. When I try to fix this on PyMOL or Python nothing seems to work, I have also tried manually editing the PDB file on Notepad but the protein is too big to go through every single calcium ion, is there a way to fix this problem? I have obtained my PDB file from the RSBC protein data bank, is there a way to download this so that it does not show so many issues on HADDOCK?
Kind regards,
Mercedes
Dear Mercedes,
Thanks for your interest in using HADDOCK for your research.
First of all, are Calcium ions important for your docking ? if not, you can remove them using the pdb_striphet function from pdb_tools to remove all HETATM in your pdb, which is often a good idea.
If they are important, you could try using python regular expression library ( re ) to match your case and modify it accordingly.
Also, the sed command in bash can do this trick.
Finally, check these two related bioexcel posts: 1, 2
With the hope that this answer will help you.
Cheers
And not all CA atoms are calcium ions! Each amino acid has a CA atom.
Only those with HETATM at the start of the line would point to calcium ions.
And as suggested already, remove anything you don’t need.