Hello,
Unfortunately, it won’t let me add a photo here. But with some PDBs (unedited from PDB website) that I add onto the Haddock2.4 website, there are multiple errors. The first being that on the next page where I have to select active residues, only some appear. So it looks something like this: R_ _ SPI _ _ _ _
I am not sure what causes this.
Any help would be much appreciated.
Thanks
Check your PDB file. There might be modified residues at those positions, not supported by HADDOCK
And never a good idea to use PDB files directly from the PDB site without checking what is inside those and removing any unneeded “junk”
Usually I remove some of the ‘junk’ via ChimeraX. Such as removing water molecules or other non standard residues. Is there an alternative method?
Or sometimes it comes up with: Error in PDB file. Your PDB contains multiple residues with number 60 in chain A or duplicated atom names.
How can I rectify this?
Thank you
Usually I remove some of the ‘junk’ via ChimeraX. Such as removing water molecules or other non standard residues. Is there an alternative method?
It’s fine as long as your remove the “junk” 
Or sometimes it comes up with: Error in PDB file. Your PDB contains multiple residues with number 60 in chain A or duplicated atom names.
This happens with high resolution crystal structures that might have multiple conformations of some side-chains.
You will have to select one per side-chain.
Our pdb-tools pdb_selaltloc can do that
Thank you, I did this then went to add the pdb again but when I submit that tab it comes up with: Error in PDB file. Unknown error: list index out of range
How can this be rectified?
Thank you
Did you use our pdb-tools to correct the PDB file?
Unfortunately not. After using the pdb tool and trying to put it in the docking again it comes up with this message: Error in PDB file. Unknown error: list index out of range
Try adding a pdb_tidy final step when preparing your PDB file
And/or share your PDB file