Haddock server cannot recognize the residue names/numbers of the submitted pdb file for a small molecule (I got the error message below). Is there a way to modify the pdb file to make it compatible with Haddock.
Thank you in advance
(Note: I am a beginner and have no prior knowledge in using Haddock)
"There was an inconsistency in your data
Error message
First pdb file contains multiple residues with number 0 in chain"
The atom names must be unique within one molecule!
You can use our PDB-tools web server to do it.
Check: https://bianca.science.uu.nl/pdbtools/manual#pdb_uniqname
Thank you very much. It works for the small molecule pdb file, but I got another error message for the DNA pdb file. It does not recognize DC as cytocine (see below). What is the suitable order to use in order to correct the pdb file?
Thanks again.
Second pdb file contains an unknown amino acid or nucleic acid base DC
Make sure to use three letter code for bases and amino acid
Thank you very much. It works for the small molecule pdb file, but I got another error message for the DNA pdb file. It does not recognize DC as cytocine (see below). What is the suitable order to use in order to correct the pdb file?
Did you define the molecule as nucleic acid?
Also check that the residue name is at the correct column - compare with a PDB file from the PDB database
-Yes, it was defined as DNA.
-They are using DC for cytocine, but the format of the PDB file in the database is different. I saved my file as pdb using Discovery Studio. Is there a way to make it similar to the database PDB format?
-They are using DC for cytocine, but the format of the PDB file in the database is different. I saved my file as pdb using Discovery Studio. Is there a way to make it similar to the database PDB format?
May-be you can read it and export it again (as PDB format) with Chimera, or PyMol
Or use some script / command line editing (e.g. with sed)
I used Chimera and PyMol to export the pdb file, but I got the same messag:
There was an inconsistency in your data
Error message
Second pdb file contains an unknown amino acid or nucleic acid base DC
Make sure to use three letter code for bases and amino acid
The pdb generates two letter code for the DNA bases (DC, DT, DG, and DA), but according to the error message, it needs three letter code.
Are you using the “old” 2.2 webserver? It indeed required three letter code residue names.
Try instead the new 2.4 server - https://wenmr.science.uu.nl/haddock2.4 - it uses the 1 / 2 letter code convention for RNA / DNA
Thank you for your help. Really appreciated.
I used Haddock 2.4, but now I faced another error message :
“The following error occurred when processing one of your PDB file: Unable to generate topology for ligand LRA. PRODRG did not create the required output:”
What is this ligand? Does it contain a metal ion (not supported)?
Its a heterocyclic aromatic compound. No metal ions.
Try deleting all hydrogen - this sometimes makes it work…