I am trying to dock small molecules with my protein. Sorry this might seem a basic question but I am struggling to prepare the pdb file for the small molecule.
I have a small molecule in pdb format. When uploaded to the web server I receive this error message “Your PDB contains multiple residues with number 0 in chain or duplicated atom names.”
Sorry I can’t find anything in a tutorial and I’m not sure what changes need to be made to the pdb text file to fix this. If you have any advice that would be great.
Thank you, I renumbered the atoms in the text file and now it works. The next problem however is the on the in put parameters page. I need to pick active residues. The only residue available for the ligand is ‘x’ and the webserver won’t allow this as a selection. How do I get passed this? (I have uploaded an image to help explain what I mean.
Sorry please ignore that last question. I realised I was typing ‘x’ rather than ‘0’!!!
However, I am having a problem selecting the ‘x’ residue for my protein which is an iron. important for ligand binding. The error says ‘none of the active residues are accessible’ when I try to select the iron. I know it is accessible as things bind to it, is there anything I can do to help the programme recognise this?
