# Residues numbering in PDB file **URL:** \ **Category:** HADDOCK\ **Created:** [December 23, 2020, 10:12am UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751 "2020-12-23T10:12:34Z")\ **Posts on this page:** 13\ **Page:** 1
**Author:** ![halniss](https://avatars.discourse-cdn.com/v4/letter/h/e5b9ba/32.png) [@halniss](https://ask.bioexcel.eu/u/halniss)\ **Post date:** [December 23, 2020, 10:12am UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751/1 "2020-12-23T10:12:35Z")
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" ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [December 23, 2020, 10:34am UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751/2 "2020-12-23T10:34:02Z")
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](https://bianca.science.uu.nl/pdbtools/manual#pdb_uniqname) ---
**Author:** ![halniss](https://avatars.discourse-cdn.com/v4/letter/h/e5b9ba/32.png) [@halniss](https://ask.bioexcel.eu/u/halniss)\ **Post date:** [December 23, 2020, 11:56am UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751/3 "2020-12-23T11:56:59Z")
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 ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [December 23, 2020, 12:13pm UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751/4 "2020-12-23T12:13:59Z")
> 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 ---
**Author:** ![halniss](https://avatars.discourse-cdn.com/v4/letter/h/e5b9ba/32.png) [@halniss](https://ask.bioexcel.eu/u/halniss)\ **Post date:** [December 23, 2020, 12:29pm UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751/5 "2020-12-23T12:29:23Z")
-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? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [December 23, 2020, 12:42pm UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751/6 "2020-12-23T12:42:29Z")
🙂 > -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) ---
**Author:** ![halniss](https://avatars.discourse-cdn.com/v4/letter/h/e5b9ba/32.png) [@halniss](https://ask.bioexcel.eu/u/halniss)\ **Post date:** [December 23, 2020, 12:59pm UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751/7 "2020-12-23T12:59:07Z")
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 ---
**Author:** ![halniss](https://avatars.discourse-cdn.com/v4/letter/h/e5b9ba/32.png) [@halniss](https://ask.bioexcel.eu/u/halniss)\ **Post date:** [December 23, 2020, 1:05pm UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751/8 "2020-12-23T13:05:31Z")
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. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [December 23, 2020, 1:28pm UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751/9 "2020-12-23T13:28:59Z")
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](https://wenmr.science.uu.nl/haddock2.4) - it uses the 1 / 2 letter code convention for RNA / DNA ---
**Author:** ![halniss](https://avatars.discourse-cdn.com/v4/letter/h/e5b9ba/32.png) [@halniss](https://ask.bioexcel.eu/u/halniss)\ **Post date:** [December 23, 2020, 1:41pm UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751/10 "2020-12-23T13:41:38Z")
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:” ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [December 23, 2020, 2:27pm UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751/11 "2020-12-23T14:27:24Z")
What is this ligand? Does it contain a metal ion (not supported)? ---
**Author:** ![halniss](https://avatars.discourse-cdn.com/v4/letter/h/e5b9ba/32.png) [@halniss](https://ask.bioexcel.eu/u/halniss)\ **Post date:** [December 23, 2020, 2:29pm UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751/12 "2020-12-23T14:29:49Z")
Its a heterocyclic aromatic compound. No metal ions. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [December 23, 2020, 2:41pm UTC](https://ask.bioexcel.eu/t/residues-numbering-in-pdb-file/2751/13 "2020-12-23T14:41:33Z")
Try deleting all hydrogen - this sometimes makes it work…