Preparing small molecules for docking

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

All atom names must be unique

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.

Thank you

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?

Thank you

If you ask for elevated access level in your registration page you can turn off the option to filter out buried residues.

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