# Problems in running HADDOCK with an amidated peptide at c-terminus

**URL:** <https://ask.bioexcel.eu/t/problems-in-running-haddock-with-an-amidated-peptide-at-c-terminus/3741>\
**Category:** HADDOCK\
**Created:** [May 31, 2022, 1:05pm UTC](https://ask.bioexcel.eu/t/problems-in-running-haddock-with-an-amidated-peptide-at-c-terminus/3741 "2022-05-31T13:05:54Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![alex](https://avatars.discourse-cdn.com/v4/letter/a/db5fbb/32.png) [@alex](https://ask.bioexcel.eu/u/alex)\
**Post date:** [May 31, 2022, 1:05pm UTC](https://ask.bioexcel.eu/t/problems-in-running-haddock-with-an-amidated-peptide-at-c-terminus/3741/1 "2022-05-31T13:05:54Z")

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I’m trying to do a job in HADDOCK with an amidated peptide in the c-terminus. However, I can’t because the following message always appears: "The following error occurred when processing one of your PDB file: Unable to generate topology for ligand NHH. PRODGR did not create the required output. PRODGR\> WARNING: deleted hydrogen H1 from your input.PRODGR\> WARNING: deleted hydrogen H2 from your input.

What can i do in this situation?

Thanks

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**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:** [May 31, 2022, 6:37pm UTC](https://ask.bioexcel.eu/t/problems-in-running-haddock-with-an-amidated-peptide-at-c-terminus/3741/2 "2022-05-31T18:37:04Z")

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Add one additional residue to your PDB file and change its residue name to CTN

See [HADDOCK Web Server - Settings](https://bianca.science.uu.nl/haddock2.4/library)

And simply defined as ATOM and not HETATM

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<div class="post-metadata">

**Author:** ![alex](https://avatars.discourse-cdn.com/v4/letter/a/db5fbb/32.png) [@alex](https://ask.bioexcel.eu/u/alex)\
**Post date:** [June 2, 2022, 12:52am UTC](https://ask.bioexcel.eu/t/problems-in-running-haddock-with-an-amidated-peptide-at-c-terminus/3741/3 "2022-06-02T00:52:10Z")

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Sorry, I did not understand how to do this. I’ve recently started using HADDOCK

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<div class="post-metadata">

**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:** [June 2, 2022, 6:35am UTC](https://ask.bioexcel.eu/t/problems-in-running-haddock-with-an-amidated-peptide-at-c-terminus/3741/4 "2022-06-02T06:35:36Z")

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Add one amino acid to your peptide (e.g. can be done in PyMol, adding one GLY residue), edit the PDB file with a text editor the file and change its name to CTN

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<div class="post-metadata">

**Author:** ![alex](https://avatars.discourse-cdn.com/v4/letter/a/db5fbb/32.png) [@alex](https://ask.bioexcel.eu/u/alex)\
**Post date:** [June 2, 2022, 10:39am UTC](https://ask.bioexcel.eu/t/problems-in-running-haddock-with-an-amidated-peptide-at-c-terminus/3741/5 "2022-06-02T10:39:10Z")

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OK. And after doing that, how do I set it as atom and not to HETATM ?

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<div class="post-metadata">

**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:** [June 2, 2022, 11:05am UTC](https://ask.bioexcel.eu/t/problems-in-running-haddock-with-an-amidated-peptide-at-c-terminus/3741/6 "2022-06-02T11:05:25Z")

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Edit the PDB file simply. It’s an ASCII text file.

When doing that make sure to keep the right column order