2021-10-14 AM1 Studies Meeting notes

General updates

• JW – Added AM1 rearrangement handlign to infrastructure roadmap - I know this is on CD’s backburner, I’ll probably get to it myself in a while.

• CD – Any update on possible project handling post-translational modificaitons?

  • JW – We’re building out the infrastructure that will be required to start looking into that. I’ll know more in a few weeks.

• JW – I can’t make this meeting time next week

  • CD – Let’s make this every-other-weekly

  • JW – Agree, I will have schedule conflicts every other week at this time.

  • JW updated the event to be every-other-weekly

Todos from last time

• Connor will see if there’s a way to expand RDKit conformer generation energy window to allow better candidate ELF conformers to be generated.

  • CD – The only thing you have to do to get RDKit to generate way more conformers is to set the min RMSD to 0, and use max_conformers to control the number of outputs instead.

  • JW – Do we know whether these output conformers are substantially distinct?

  • CD – I suspect they are but haven’t verified. What you could do is generate more conformers than you want, and then prune them by diversity.

  • LW – I know that RDKit generates a alrge umber of conformers internally and then prunes them, possibly using the provided RMSD, util the desired number of conformers is achieved.

  • LW – Can we set an energy window in RDKit?

    • JW – I think we’d looked into this a little last time, and I don’t think we found a way to set this.

    • LW – I have some code that prunes conformers by an energy window that I specify (calculating energies using MMFF)

  • CD – Shows plot of ELF1 comparison now that RDKit is generating way more conformers

• JW – I look at the bottom plot in terms of “should we throw out the current random conformer selection and implement ELF1 immediately?”, and the data is making me think “no”

• Connor will evaluate whether OE vs. antechamber charge differences correlate with RMSD

Next steps