# Pdb file contains an unknown amino acid or nucleic acid base U
**URL:** https://ask.bioexcel.eu/t/pdb-file-contains-an-unknown-amino-acid-or-nucleic-acid-base-u/323
**Category:** HADDOCK
**Created:** [March 17, 2017, 4:33pm UTC](https://ask.bioexcel.eu/t/pdb-file-contains-an-unknown-amino-acid-or-nucleic-acid-base-u/323 "2017-03-17T16:33:46Z")
**Posts on this page:** 8
**Page:** 1
### Author:  [@111](https://ask.bioexcel.eu/u/111)
#### Post date: [March 17, 2017, 4:33pm UTC](https://ask.bioexcel.eu/t/pdb-file-contains-an-unknown-amino-acid-or-nucleic-acid-base-u/323/1 "2017-03-17T16:33:46Z")
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to [http://www.bonvinlab.org/software/haddock2.2](http://www.bonvinlab.org/software/haddock2.2)
Dear developers,
I run a protein RNA docking. But i found the following error:
Second pdb file contains an unknown amino acid or nucleic acid base U
Make sure to use three letter code for bases and amino acid
How do I solve this problem?
Thank you!
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### Author:  [@mtrellet](https://ask.bioexcel.eu/u/mtrellet)
#### Post date: [March 17, 2017, 4:50pm UTC](https://ask.bioexcel.eu/t/pdb-file-contains-an-unknown-amino-acid-or-nucleic-acid-base-u/323/2 "2017-03-17T16:50:01Z")
Hello,
Just replace the “U” by “ **URI** ” (and not URA) in your residue name column 😉 HADDOCK needs three letter code to parse and read PDB files.
Good luck!
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### Author:  [@111](https://ask.bioexcel.eu/u/111)
#### Post date: [March 18, 2017, 3:01am UTC](https://ask.bioexcel.eu/t/pdb-file-contains-an-unknown-amino-acid-or-nucleic-acid-base-u/323/3 "2017-03-18T03:01:55Z")
Thank you. But how can I replace the “U” by “URA” in my PDB files?
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [March 18, 2017, 9:09am UTC](https://ask.bioexcel.eu/t/pdb-file-contains-an-unknown-amino-acid-or-nucleic-acid-base-u/323/4 "2017-03-18T09:09:47Z")
First the correct name should be URI and not URA
Second: edit your file… or use some sed command on Linux
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### Author:  [@111](https://ask.bioexcel.eu/u/111)
#### Post date: [March 20, 2017, 7:14am UTC](https://ask.bioexcel.eu/t/pdb-file-contains-an-unknown-amino-acid-or-nucleic-acid-base-u/323/5 "2017-03-20T07:14:59Z")
> [@amjjbonvin](#):
>
> Second: edit your file… or use some sed command on Linux
Thank you very much! I tried a few times, but failed. The following error:
Second pdb file is incorrectly formatted. Please align the columns of your PDB properly.
Can you help me convert the “U” to “URI” in the pdb file?
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [March 21, 2017, 9:12am UTC](https://ask.bioexcel.eu/t/pdb-file-contains-an-unknown-amino-acid-or-nucleic-acid-base-u/323/6 "2017-03-21T09:12:34Z")
The residue name in a PDF file should be placed in columns 18-20
When editing your file make sure to replace the U + two space by URI (and check which spaces should be replace (before or after U).
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### Author:  [@111](https://ask.bioexcel.eu/u/111)
#### Post date: [March 22, 2017, 9:01am UTC](https://ask.bioexcel.eu/t/pdb-file-contains-an-unknown-amino-acid-or-nucleic-acid-base-u/323/7 "2017-03-22T09:01:42Z")
Hi amjjbonvin,
Thank you for your help. I have replaced “U” by “URI”. However, my HADDOCK run sitill could’t be processed. The error:
Second pdb file **contains an unknown amino acid or nucleic acid base G** Make sure to use three letter code for bases and amino acid
All bases need to be replaced with specific symbols?
Best
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [March 22, 2017, 9:15am UTC](https://ask.bioexcel.eu/t/pdb-file-contains-an-unknown-amino-acid-or-nucleic-acid-base-u/323/8 "2017-03-22T09:15:32Z")
Yes - all bases!
A -\> ADE
T -\> THY
C -\> CYT
G -\> GUA
U -\> URI