A worldwide e-Infrastructure for NMR and structural biology

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locating the chosen pdb models within the tgz file



I have ran HADDOCK and I received the webpage with the best clusters (including the pdb files). 

I have also downloaded the full tgz dataset resulting from the run. I was trying to locate the pdb files belonging to the best clusters within that dataset, but I could not find them. I was searching in structures/t1. This folder contains 200 pdb models, but none of them matched the pdb files mentioned in the clusters shown on the results webpage.

Issue status: 

Definition of the interface-ligand RMSD

I was wondering how the interface-ligand RMSD used for the clustering of the water-refined models is defined.

The web server tutorial defines both the interface RMSD and the ligand RMSD (see below), but does not specify how the combination of both is calculated.

Issue status: 

Normalized HADDOCK score

I was wondering whether the HADDOCK score is comparable over multiple runs using the same molecules but different active residues or whether it can only be used for comparing structures generated in a single run. Is it normalized over the amount of AIRs defined for the docking?

Thanks in advance!

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How to name DNA/RNA for HADDOCK

The HADDOCK Webserver could only identify three-letter DNA/RNA name in a pdb file.

How to change the name? Thanks.

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HADDOCK2.2 fails with a %ATMCHK-ERR error in the simulated annealing stage of the docking

Dear HADDOCK team,

How to solve this problem?

I am trying to model a protein-DNA complex by docking. I am using the Expert interface of the HADDOCK2.2 web server. During the the simulated annealing stage HADDOCK2.2 fails with an error message from CNS as follows:

Issue status: 

Error supplied an unknown user name

Dear HADDOCK team,

recently i submitted for a HADDOCK account and today i got my username along with a password. As i wanted to run HADDOCK with my username jonathankordon the error "supplied an unknown user name" appeared. Thanks in advance.




Issue status: 

Haddock run on UBUNTU apparently stuck (finished?) AND error in hydrophobic contact analysis

Dear members,

I am trying to test run haddock2.2 on UBUNTU using the /examples/protein-protein data.

1. After some tinkering, the program apparently executed properly but seems to be stuck now apparently in the 'analysis' (the analysis directory is present in /it1 and /it1/water).

2. An additional concern is that while execution, the program reports a syntax error in a count_hbonds.awk file and and error in hydrophobic contact analysis. 

3. What does the prompt "[1]  + Killed" mean?

Issue status: 

Stuck in semi-flexible refiment (it1)

Dear Haddock team,

I have a problem in it1, but the previous iteration (rigid body), it0, seems ok.

I have posted the haddock output, and also the files used to generate the run.

Xiong An


#### Haddock2.2 OUTPUT Iteration1####

Issue status: 

HADDOCK 2.2 stuck in 'waiting for psf files ...'

Dear members,

I recently installed HADDOCK 2.2 on mac osx (Yosemite) as well as UBUNTU. I am trying to go through the 'protein-protein' docking  example on both machines. The program seems to be stuck in 'waiting for psf files ...' Below is the execution log of run1. Any help in this would be appreciated.


% haddock2.2

Issue status: 


Dear HADDOCK-Team,

I am very thankful for your website. It is such a great help.

Recently - a week ago to be more precise - I have submitted 2 proteins for a docking run.

A day later, the run has started. Unfortunately, every time, ever since, that I check the status of my run, I have the feeling that it is not progressing anymore. Is it possible that the run has crashed? Should I resubmit it? 

I may just be too impatient. In such a case, sorry for any inconvenience.

Many thanks in advance for your reply!

Issue status: 

Cite WeNMR/WestLife

Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
"The FP7 WeNMR (project# 261572), H2020 West-Life (project# 675858) and the EOSC-hub (project# 777536) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, Taiwan and the US Open Science Grid."
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.


The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858