# Capping residues

**URL:** <https://ask.bioexcel.eu/t/capping-residues/4445>\
**Category:** HADDOCK\
**Created:** [August 6, 2023, 2:28pm UTC](https://ask.bioexcel.eu/t/capping-residues/4445 "2023-08-06T14:28:34Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![Miriam](https://avatars.discourse-cdn.com/v4/letter/m/c89c15/32.png) [@Miriam](https://ask.bioexcel.eu/u/Miriam)\
**Post date:** [August 6, 2023, 2:28pm UTC](https://ask.bioexcel.eu/t/capping-residues/4445/1 "2023-08-06T14:28:34Z")

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Hi  
Is it possible to put capping residues on the N and C terminus of a peptide using haddock tools like the pdb\_mutate.py code or a different way? (using local version)  
I see haddock knows ACE but I don’t want to mutate the entire amino acid to ACE, just the cap.  
Or do I have to use a different program such as pymol?  
Thx  
Miriam

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<div class="post-metadata">

**Author:** ![Miriam](https://avatars.discourse-cdn.com/v4/letter/m/c89c15/32.png) [@Miriam](https://ask.bioexcel.eu/u/Miriam)\
**Post date:** [August 6, 2023, 3:23pm UTC](https://ask.bioexcel.eu/t/capping-residues/4445/2 "2023-08-06T15:23:03Z")

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I want it to be aceteylated and amidated, not just uncharged

Also, when I used “protein-allhdg-5-4-noter.link” on molecule 1 and 2  
like this  
{\* linkage file for molecule 1 _}  
{===\>} prot\_link\_mol1=“protein-allhdg5-4-noter.link”;  
{_ linkage file for molecule 2 \*}  
{===\>hi} prot\_link\_mol2=“protein-allhdg5-4-noter.link”;

the results gave output that have a charged end.  
why? did I do something wrong?

Best,  
Miriam

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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:** [August 6, 2023, 5:50pm UTC](https://ask.bioexcel.eu/t/capping-residues/4445/3 "2023-08-06T17:50:20Z")

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Define charged

What are the atoms present at the N- and C-ter?

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<div class="post-metadata">

**Author:** ![Miriam](https://avatars.discourse-cdn.com/v4/letter/m/c89c15/32.png) [@Miriam](https://ask.bioexcel.eu/u/Miriam)\
**Post date:** [August 6, 2023, 6:55pm UTC](https://ask.bioexcel.eu/t/capping-residues/4445/4 "2023-08-06T18:55:50Z")

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For example I want NME aspartic acid and ACE proline

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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:** [August 6, 2023, 10:00pm UTC](https://ask.bioexcel.eu/t/capping-residues/4445/5 "2023-08-06T22:00:47Z")

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Not the answer to my question…

You said that when using the noter linkage files you have charged termini.

Do again what are the termini atoms? There should not be a charge in case

I will answer the capping questions it the other thread

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<div class="post-metadata">

**Author:** ![Miriam](https://avatars.discourse-cdn.com/v4/letter/m/c89c15/32.png) [@Miriam](https://ask.bioexcel.eu/u/Miriam)\
**Post date:** [August 7, 2023, 7:00am UTC](https://ask.bioexcel.eu/t/capping-residues/4445/6 "2023-08-07T07:00:52Z")

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I did noter linkage when on the N termini was proline and C termini aspartic acid.  
In the output it looks charged

 ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/ed66a240cf7a6b98c783ffaba968b0c8fb8e86af.png)

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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:** [August 7, 2023, 8:01am UTC](https://ask.bioexcel.eu/t/capping-residues/4445/7 "2023-08-07T08:01:26Z")

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Ok - you indeed found an issue for the N-terminal proline (will correct it).

If you want to test things on your side, edit the `protein-allhdg-5.4-noter.link` file and delete at the end of the file the following lines:

```auto
first PROP tail + PRO end
first PROP tail + HYP end
first PROP tail + HY3 end

```

As for the C-ter, it is uncharged. What you are seeing in the picture is the side-chain carbonyl. The C-ter carbonyl only has a C=O group

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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:** [August 7, 2023, 8:03am UTC](https://ask.bioexcel.eu/t/capping-residues/4445/8 "2023-08-07T08:03:41Z")

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The way to do is it to add two additional GLY residues, one at the beginning and one at the end (e.g. using PyMol).  
And then rename the N-ter one (the first residue) to NME and the C-ter one (the last one) to ACE.

HADDOCK will discard any unneeded atom and build the missing ones.