Hi,
I am following " Cyclization and Docking Protocol for Cyclic Peptide–Protein Modeling Using HADDOCK2.4 ". To cyclize linear peptide in the paper, it said "single-molecule mode in the cyclization protocol to generate the cyclized peptides " but on haddock2.4 web server there is no option for number of molecules as 1, it starts from 2. So I am wondering if you could please help me with this. Thank you very much.
Dear jin.
I am not sure about how to perform this with haddock2.4.
But with haddock3, we have dedicated examples that can be followed and should be functional.
Here are the links:
For the full explanation of how to perform this with haddock2.4, someone else from our team will help you.
Best regards.
This was done using the command line version of haddock2.4
Thank you very much!
Thank you very much. May I ask it take to get approval for download access for haddock2.4. I submitted request from Obtaining HADDOCK – Bonvin Lab but not get reply yet. I am worried if my email was wrong. So I am wondering if there is any email address I can ask about it. Thank you very much!
Hi,
Thank you very much for help.
I am running cyclization step of peptide on local version of haddock2.4.
Now I want to run ana_structures.csh scripts under run1/tools
the command to run ana_structures.csh in toturial is as follows:
$HADDOCKTOOLS/ana_structures.csh
in my system is “csh ana_structures.csh”. and I have csh installed. But I got some error message as follows:
cat: file.nam: No such file or directory
head: cannot open ‘file.nam’ for reading: No such file or directory
I looked at ana_structures.csh script there is not code to set variable file.nam
I automatically got tools/ana_structures.csh after call haddock2.4.
I am wondering if you could please take a look for my ana_structures.csh script. Thank you very much for your help.
ana_structures.txt (6.0 KB)
I am running cyclization step of peptide on local version of haddock2.4.
Now I want to run ana_structures.csh scripts under run1/tools
the command to run ana_structures.csh in toturial is as follows:
$HADDOCKTOOLS/ana_structures.csh
in my system is “csh ana_structures.csh”. and I have csh installed. But I got some error message as follows:
cat: file.nam: No such file or directory
head: cannot open ‘file.nam’ for reading: No such file or directory
Are you running it in a directory where the PDB files are and in particular file.nam is located (structurte/it1, structures/it1 and structures/it1/water
Thank you very much for help. I know why I get errors. I should run the script under structurte/it1.
I have another questions. In the step 3 of cyclization of peptide. I used ten representative structures from the first 10 clusters of step2 results. First, I am wondering if I should use cluster center for each cluster. Second, Whether I use results from structures/ it1 or structures/it1/water. As I found cluster center is very different for first ten clusters under these two directories. Thank you so much for your help.
Dear Jin
I would suggest to take a look at the new HADDOCK3 version.
[
It can now be installed simply with pip install haddock3
We have in it an example of a workflow for peptide cyclisation that does it all in one go 
[
|
haddock3/examples/peptide-cyclisation at main · haddocking/haddock3 |
I have another questions. In the step 3 of cyclization of peptide. I used ten representative structures from the first 10 clusters of step2 results. First, I am wondering if I should use cluster center for each cluster. Second, Whether I use results from structures/ it1 or structures/it1/water. As I found cluster center is very different for first ten clusters under these two directories. Thank you so much for your help.
We used the water models, selecting the top model of the top50 clusters typically
Check the details in the paper
Cheers
Alexandre
Thank you so much for your help and time. I found the workflow in haddock3 make life much easier! Thank you very much for letting me know that. I am really appreciated! I have three questions and I am wondering if you could please help mw with this. I would be much appreciated.
- I download haddock3 from github. I found from this instructions CNS Installation — haddock3 3.0.0 documentation . It said that cns needed to be recompiled and added the newly generated *exe to haddock3/bin and renamed it as cns. But I cannot found a bin directory under haddock3 after installation. I am wondering if you could please help me with this.
- Under examples/peptide-cyclisation, I guess 3wne_unambig.tbl is the restraint file for head to tail cyclization. May I use the parameter for distance, upper-bound correction, lower-bound correction in 3wne_unambig.tbl for my peptide. I want head to tail cyclization for my peptide as well but I do not know how to generate distance restraint file for single molecule.
- I found under haddock3/examples/peptide-cyclisation/data there are two pdb files for 3wne.
“3wne_peptide-bound.pdb” and “3wne_peptide-ensemble.pdb” for 3wne_peptide-bound.pdb I guess it is the cyclic form coming from a bound complex. But for my case I do not have my peptide in cyclic form from bound complex. So I am wondering how I could modify cyclise-peptide-3wne-full.cfg file. - last but not least may I ask how do I execute the cyclise-peptide-3wne-full.cfg as I did not found usage instructions in the file.
Thanks again
Jin
Try simply a pip install haddock3 (after you created either a Python venv or a conda environment.
This installation should have CNS in it
- No need to compile CNS anymore,
pip install haddock3will download a pre-compiled executable - Yes, use the provided distance parameter, but adapt it to your system. But make sure you update it to the correct residue names and indices.
“3wne_peptide-bound.pdb”is the reference structure / the target conformation found in the PDB. In the workflow we cyclisize the“3wne_peptide-ensemble.pdb”peptide conformations, generated by pymol- to execute it, simply run
haddock3 cyclise-peptide-3wne-full.cfg
- Under examples/peptide-cyclisation, I guess 3wne_unambig.tbl is the restraint file for head to tail cyclization. May I use the parameter for distance, upper-bound correction, lower-bound correction in 3wne_unambig.tbl for my peptide. I want head to tail cyclization for my peptide as well but I do not know how to generate distance restraint file for single molecule.
You can use those indeed, but adapt the residue numbering to your case.
- I found under haddock3/examples/peptide-cyclisation/data there are two pdb files for 3wne.
“3wne_peptide-bound.pdb” and “3wne_peptide-ensemble.pdb” for 3wne_peptide-bound.pdb I guess it is the cyclic form coming from a bound complex. But for my case I do not have my peptide in cyclic form from bound complex. So I am wondering how I could modify cyclise-peptide-3wne-full.cfg file.
The bound one is the reference conformation in the complex, just as a reference to measure how well the cyclisation protocol is working.
Not needed in your side (you can remove the reference to it in the cfg file.
The 3wne_peptide-ensemble.pdb contains an ensemble of initial conformations for the peptide built with PyMol.
- last but not least may I ask how do I execute the cyclise-peptide-3wne-full.cfg as I did not found usage instructions in the file.
haddock3 cyclise-peptide-3wne-full.cfg
Thank you so much for your kind help. I am really appreciated. I have another two questions and am wondering if you could please help mw again.
- I want to check with you. I comment out 'reference_fname = “data/3wne_peptide-bound.pdb” ’ in cyclise-peptide-3wne-full.cfg. I am wondering if I need to comment out '[caprieval] ’ in cyclise-peptide-3wne-full.cfg.
- I installed haddock3 with " pip install haddock3" and was able to call “haddock3 -h” but when I started with a new terminal I cannot successfully call “haddock3 -h”. Now I want to add haddock3 to PATH. I am wondering under which directory the executable for haddock3 located.
Thank you so much for your kind help. I am really appreciated. I have another two questions and am wondering if you could please help mw again.
- I want to check with you. I comment out 'reference_fname = “data/3wne_peptide-bound.pdb” ’ in cyclise-peptide-3wne-full.cfg. I am wondering if I need to comment out '[caprieval] ’ in cyclise-peptide-3wne-full.cfg.
You can either only comment out the ‘reference_fname’ line (in that case the analysis will be performed with respect to the best (top-ranked) model, or remove completely the caprieval block.
- I installed haddock3 with " pip install haddock3" and was able to call “haddock3 -h” but when I started with a new terminal I cannot successfully call “haddock3 -h”. Now I want to add haddock3 to PATH. I am wondering under which directory the executable for haddock3 located.
How did you install it? With conda, or in a venv?
You will have to activate the environment first to have haddock3 in your path.
Thank you very much. I got haddock3 run. Now I met an error message and I am not sure.
I am wondering if something wrong with cns.
[2024-11-04 16:07:16,224 libparallel WARNING] Exception in task execution: b’/home/micromamba/envs/haddock3/lib/python3.9/site-packages/haddock/bin/cns: error while loading shared libraries: libmvec.so.1: cannot open shared object file: No such file or directory\n’
[2024-11-04 16:07:16,226 libparallel WARNING] Exception in task execution: b’/home/micromamba/envs/haddock3/lib/python3.9/site-packages/haddock/bin/cns: error while loading shared libraries: libmvec.so.1: cannot open shared object file: No such file or directory\n’
[2024-11-04 16:07:16,230 libparallel INFO] 2 tasks finished
[2024-11-04 16:07:16,231 init INFO] [topoaa] CNS jobs have finished
[2024-11-04 16:07:16,232 libutil ERROR] 100.00% of output was not generated for this module and tolerance was set to 0.00%.
Hi there
I think we have an issue with the cns version coming via pypi. I will assume you are installing haddock3 on a Linux system.
Try the following:
rm /home/micromamba/envs/haddock3/lib/python3.9/site-packages/haddock/bin/cns
Go in the haddock3 installation directory directory (assuming you cloned it from git before) and type:
`pip install .`
This should reinstall the missing cns version (and hopefully a working one).
Hi,
Thank you very much for your help.
May I ask to run cyclic peptide protein docking as described in the paper. I am wondering which one you suggest to run docking, the haddock2.4 webserver or local version.
Also, for the local version to run docking on local version. May I use haddock3 on haddock3/examples/peptide-cyclisation at main · haddocking/haddock3 · GitHub.
For the parameters to run docking of cyclic peptide if the run.cns provided in the paper is enough.
Thank you very much for help
Best regards
For the docking, you can use the server. You will need expert access in order to specify the peptide to be considered as cyclic.