Capping residues

Is it possible to put capping residues on the N and C terminus of a peptide using haddock tools like the 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?

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

Also, when I used “” on molecule 1 and 2
like this
{* linkage file for molecule 1 }
{===>} prot_link_mol1=“”;
linkage file for molecule 2 *}
{===>hi} prot_link_mol2=“”;

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


Define charged

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

For example I want NME aspartic acid and ACE proline

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

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

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 file and delete at the end of the file the following lines:

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

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.