Using metal ions as an input structure

Hi everyone,
I’m trying to use HADDOCK to help me build some models of a protein of my interest. After building the initial model I need to ressemble a multimeric protein that builds a metal binding site on one of the interfaces (after experimental data). As I don’t know for sure the metal binding pocket conformation I was hoping in using the ion as a third structure with restraints between monomers and between monomers and the metal ions. The thing is that the first iteration works ok, making some interesting models, but the refinement iteration just crashes at the point of building the covalent bond between the protein and the metal ion. It seems that the covalions.cns script looks only in the same SEGID to build the bond. Could this be changed so that in case the metal ion doesn’t belong to any protein structure in particular, it just builds a bond with the closes coordinating atom from the other SEGID? I’ve rerun the docking including the ion in one of the protein models, and it works just fine, but the results aren’t as interesting as the ones I got using multi-body docking. Thanks in advance!

The ion being an isolated atom will indeed give problems in the refinement stage in torsion angle dynamics.

One possible solution is to set the number of steps to 0 for all it1 stages (advanced sampling options if you use the server - run.cns for a local run). Only water refinement will then be performed in this case with some flexibility.

Dear Dr. Bonvin,
Thanks for the prompt answer. Just so you know, I tried what you suggested, but it seems that setting the it1 steps to 0 avoids any refinement altogether, ending with “Number of structures for iteration 1 is zero.”. Am I missing something?
Best regards,

You must have changed the wrong parameters…

Looking in run.cns for the following lines and set the number of steps to 0:

{* number of MD steps for rigid body high temperature TAD *}
{===>} initiosteps=500;

{* number of MD steps during first rigid body cooling stage *}
{===>} cool1_steps=500;

{* number of MD steps during second cooling stage with flexible side-chains at interface *}
{===>} cool2_steps=1000;

{* number of MD steps during third cooling stage with fully flexible interface *}
{===>} cool3_steps=1000;

PS: If you have a local install, I might have to send you an updated version for this to work with isolated ions.

Dear Dr. Bonvin,
If I change only those parameters, I get the same error for the
metal-residue bond not being able to be formed, so it seems haddock runs
the script at the beginning of it1, even with 0 steps, and that also any
water refinement depends on it1, am I right? I indeed have a local
installation, so tell me if you want me to test the new version.
Best regards,