Capping residues

HADDOCK
1

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

2

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

3

Define charged

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

4

For example I want NME aspartic acid and ACE proline

5

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

6

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

image
image775×114 32.6 KB

7

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:

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

8

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.