Monday, June 10, 2013

FragIt and Metals

FragIt is a tool that helps you setup a fragment calculation, more specifically for use in the Fragment Molecular Orbital (FMO) method and its Testosterone induced cousin the Effective Fragment Molecular Orbital (EFMO) method.

Since my switch to the University of Southern Denmark, FragIt's capabilities have grown a bit. Now it supports Molecular Fragmentation with Conjugate Caps so it can dump coordinate files and you can estimate interaction energies quickly and I am trying to switch to a more flexible configuration system, but that is a topic for another post on a related blog.

However, my proudest moment regarding FragIt must have been today when I finally fixed an issue with FragIt that has been haunting me for some time. Metal ions. The problem is that FragIt uses the excellent Open Babel toolkit as its underlying work horse, but the charge models that are implemented are misbehaving when metals are present (through the Python bindings). The partial charges are not present for the metals which I guess makes sense

My solution was rather elegant:

while metals are present
  • store a copy of them in a separate list
  • delete them from the system
  • calculate the partial charges of the system without the metal ions.
Finally, reinsert the metal ions and use their formal charge (which you are certainly most interested in) as the partial charge of the ion. From here, everything is as usual and you can do all your usual tricks with FragIt as you are used to.

The only catch is that whatever metal ions you want to include has to be last in whatever structure file you are using and I should mention that the web interface is not yet updated with this feature.

That's what conferences are for! Stay tuned for a 1.0.7 point release sometime in the near future.

btw - metal ions can be mispelled to say meta lions which I at this hour find rather amusing.