I've adjusted the source code of Gaussian accelerated molecular dynamics (GAMD) with OpenMM (github.com/MiaoLab20/ga...) to accept periodic molecules, such as a sequence bonded to itself across the periodic boundary.

HelicalFMO is in active dev. I'm automating the cross-angle of two helical peptides at N points on the backbone. The maths is not quite right 😅
That's enough work. Time for a 4-day break in Barcelona!

github.com/acnash/Helic...

I'm slowly collating my MD scripts on Github. They're nowhere near ready, but this is the result of code isolating just surface residues, so tools such as Autodock Vina can use them as search box centres.

github.com/acnash/MDScr...

Keeping a critical eye on my fellowship application.

I gave up. Used Python's "Pymol-open-source" package. What's one more dependency 🫠

This is a spectacular failure. It's not quite what I was after, but it's pretty nonetheless. I was hoping to avoid OpenBabel or Pymol dependencies.

Needle in a haystack. CHARMM-GUI builder placed some atoms exactly on other hands... but which ones? A short #MDAnalysis script looking for any two or more residues that share an identical (x,y,z) position should reveal the culprits. But that can wait until Monday :-)

I'm building something cool!
Membrane-bound metalloproteases.