Error in the simulated annealing stage of the docking

HADDOCK
1

Hello,

I’m trying to dock two proteins, but the run keeps failing.
I’m getting the error message:

%NOESET error encountered: exceeded NOECMX parameter --> recompile program

I can’t find any other mention of this error, any idea what it means/what I can do to fix it?
Cheers!

2

Server or local?

This is a CNS issue which will need recompiling the code.

Any special distance restraints you are defining?

3

I’m running this on the server, but haven’t set any distance restraints (left all the docking parameters as default).
How would I go about recompiling the code?

Thanks for your help.

4

You must have defined some restraints (or active residues), otherwise you would not be able to submit…

Can you share the link to your run (eventually via private email)?

5

I see you have quite a number of sulphate groups on your proteins. Do you need those?

This seems the origin of the problem (which we can probably fix). But those might be coming from the crystallization buffer and be irrelevant for the interaction, in which case it is always better to remove those (and any other irrelevant small molecule).

1 Like
6

Ah I see thank you. I’m not certain but these might just be a result of the buffer as you say.
Is there a way to do remove them with the PDB-Tools?

7

Simple to do with a simple text editor.

But PDB-Tools does have a module for it called pdf_delhetatm

https://bianca.science.uu.nl/pdbtools/manual#pdb_delhetatm

This will remove ALL hetero atoms

8

I removed the sulphate groups in Pymol (as some of the heteroatoms are important and I didn’t want them deleted) and the run has worked.

Thank you, I really appreciate your help!