Release of FragIt 1.3

I'm proud to announce the immediate availability of FragIt 1.3!

From the release notes:

 * Stabilization of the API for 3rd party uses

 * API has support for a QM-region in the XYZ-MFCC
   writer. This QM-region can be expanded by including
   covalently bound or hydrogen bound neighbours.

   This support is slated to be included more generally
   in a future fragit 1.4 release series.

 * A visually more pleasing color scheme. We are no
   longer living in an 8-bit world.

 * FragIt now exits more cleanly if it cannot find itself.

The visually more pleasing color scheme was discussed in a previous post.

Calculating Shieldings for Proteins

I'm just going to show some recent work on extending the Polarizable Embedding from being a focused QM/MM model into an approach to generate parameters for entire proteins or DNA. Here is a snapshot of the human protein GB3 (PDB: 2OED) with the central QM-fragment we are interested in - here LYS4 - shown in vdw-spheres. Also in the QM-region are neighbouring residues and stuff (side-chains and water) that binds to the central fragment of interest) all highlighted in cyan in sticks. The rest of the protein along with a lot of water is the MM-region. Only the protein is shown in a classical cartoon rendering.

Enjoy

FragIt has a better look!

Active development with FragIt is still going strong as I work my way through interfacing it with other software that we are building in-house to allow you to run these high-quality QM/MM calculations with relative ease.

I've just added a visually more pleasing color scheme to the development version which you can see in the image below

The old colorscheme is to the left and the new is to the right.

it just became a lot cooler to visually inspect your molecule of interest.

Release of FragIt 1.2

After a ferocious development spree, I am proud to announce the release of FragIt 1.2.

Under the hood, it has primarily been reworking some of the finer details of the API to allow for better integration with programs wishing to use it.

Directly from the release-notes:

This release provides Molcular Fragmentation with Conjugate Caps (MFCC) support through FragIt. Currently, it dumps all capped fragments and all caps as separate .xyz files so you can process them further on in the quantum chemistry code of your choice. You can access it through the writer = XYZ-MFCC option in the [fragmentation] group.
This release also includes some updated API for better integration with other codes that wants to interface with FragIt.

FragAway!

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.