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
Hi, I edit my peptide from a known pdb, using chimeraX. On there I can see that my peptide is cyclic and the disulfide bond present. After using the online Haddock2.4, I download the pdb of the top complex. When I observe it in chimeraX, I notice that the cyclic peptide no longer looks bound together and neither is the disulfide bond. Do you know what causes this and how I can change that?
Did you specify on the server that the peptide should be cyclic?
Do you have a run number for this one?
Yes I did specify cyclic peptide. This is the link to it as I am not sure on the run number
https://rascar.science.uu.nl/haddock2.4/result/9938322197/446453-HEPSIN-SFTI-V8-TRIAD
The break in the cyclic peptide is always between amino acid 1 and 14
The peptide is cyclic!
It is a visualisation artefact
switch to a sticks representation instead of ribbon and you will see it is cyclic.
In stick representation I also see the bond break but maybe that is just an issue with ChimeraX. Thank you for checking though, I just wanted to be sure that my haddock scores were accurate