While I was at the University of Cambridge, working with CCPN and building a web portal for handling NMR data, I've created ACPYPE, a tool to generate topologies for chemical compounds and to interface with others python applications like CCPN or ARIA, but it ended being a hit with GROMACS user community and I became a fan of AMBER forcefields.

Well, it happened I did work a lot with GROMACS as a graduating student back then in Rio de Janeiro, a time where I was doing a bit of everything, from compiling specific Linux kernels to studying HIV protease in silico.

It's a niche application, I know, and If not for Wim Vranken, ACPYPE would probably never have come to see the light of the day. But we came to realise it was a good thing, so I made a web portal for it as well, firstly, hosted at Cambridge, and now being hosted at Bio2Byte, Wim's group at VUB, thanks to the help of Luciano Kagami.

Yet, after CCPN, I went to work for nine years at Uniprot and ACPYPE went into a minimal maintenance mode, where I tried to keep it up with AMBER and GROMACS updates. So, after this intense time at EBI, our family took a break and went to "experiment" life in the continent. Then enters COVID... you know the rest.

I'm now in Brittany, France, working mostly as a freelance, considering going back to Cambridge, at some point, but we may try to resume our nomad life in Europe and go to Portugal, who knows.

Plans for ACPYPE

(not necessarily in order of importance)

• Automatise GROMACS residue creation (rtp file):
  so, you have a small molecule and want to convert it in a residue-like for exoteric protein simulations...
• Evaluation Amber forcefields 14SB and 19SB:
  I may end up needing to use old GROMACS versions as the modern ones don't do vacuum calculations anymore and I need it for FF validations
• Improve amber2gmx direct conversion functionality:
  I realised solvents may have some issues
• Review the whole code and bring it up to modern Python3 usage:
  For example, I may consider typing, as it may easier the integration with modern web frameworks
• Rerun ACPYPE against thousands of small compounds again:
  As we did in the original article
  ...

Sponsorship

One-off contributions are, obviously, welcome. Any recurring contributions are more than welcome. Any value is appreciated and feel free to add you requests to my TODO list.
It should not come as a surprise if I'm usually inclined to give more attention where the money is but ACPYPE reliability is the most important thing for me.
I'm opened for consultancy and contract works as well, just drop me an email.

Many thanks,

Alan Silva 🚲🏊‍♂🏃‍♂🇧🇷🇫🇷🇬🇧