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.

DALTON mol File Input Generator for Open Babel

Because of my new engagement with DALTON, I felt there was a serious lack of availability in the open source tool chain that I am used to: There is no input file generator in Open Babel for DALTON, until now.

Through a series of commits in my own fork of the official Open Babel repository, I've added a basic mol file input generator (and reader too!). The commits have been marked with a pull request to be merged into the official repository, but it looks like it is only updated every now and then. If you want to get all crazy right away, clone my repository and get cracking.

Experienced users with DALTON knows that there are two input files. the molecule file and the DALTON input file (dal file). The mol file contains the coordinates of the atoms, their charge and the basis set for the computation. The dal file tells DALTON what to actually do with the content of the mol file. Thus, the dal file is about the quantum chemistry which is traditionally left out in Open Babel and I've only focused on getting the mol-file ready - most users of DALTON use a single dal file anyways and use different mol files. I guess my own scripts to make easy conversions to and from DALTON are now void (at least partially).

Hooray for Open Source!

Addendum: I should mention that coordinates can also be extracted from DALTON log files. As I myself do not (usually) have a need beyond coordinate extractions I will leave it as is for now.

Extending FragIt for Molecular Fragmentation with Conjugate Caps

As the co-author of FragIt(web, code), a piece of software written in Python using the Open Babel API, to help setup and fragment large molecules in fragment based methods, I have to return to this (excellent) piece of software to make it work with Molecular Fragmentation with Conjugate Caps (MFCC) methods which is the approach that my new work-place has taken as their method of choice in fragment based methods. Currently, FragIt only (officially) supports the Fragment Molecular Orbital (FMO) method.

Step I of this transformation is to realize that FMO and MFCC are two very different beasts. While the theory of FMO is more hairy, the information that FMO needs to run is vastly less than MFCC. In FMO, you specify pairs of atoms between which you wish to fragment and then everything goes along nicely whereas in MFCC you build fragments, attach caps and build extra fragments from those caps (called conjugate caps). The latter is very tough to do generally which is the approach and idea of FragIt in the first place: Mostly because getting the correct SMARTS you need is very cumbersome. As with the previous approach of FragIt, I'll make it work for proteins by selecting the appropriate SMARTS and program it in such a way that extensions to other systems would be straight-forward by simply figuring out additional patterns.

Right now my approach is to build “capping”-SMARTS that select atoms around places of fragmentation and build those caps in Open Babel. Non-trivial task is non-trivial I must admit.

Stay tuned as I explore the SMARTS and code needed to accomplish this.