2022-02-03 Davel/Madin/Wagner Meeting notes

Owned by Jeffrey Wagner, created
Last updated: Feb 03, 2022
2 min read

 Date

Feb 3, 2022

 Participants

  • @Jeffrey Wagner

  • @Connor Davel

  • @Owen Madin

 Discussion topics

Item

Notes

Item

Notes

General updates

  • CD – UROP (summer fellowship) deadline is coming up (Feb 18) - It’d be great if next project could be fleshed out in time for that. Have you heard anything from MS about the writeup for this?

    • JW + OM – I haven’t heard anything from MS

    • OM + CD – These can be done pretty quickly.

    • OM will ask MS for a brief version of the project description that we can turn into a UROP proposal

  • JW – I brought up the conclusions from CD’s studies on slack, I think the issue is awaiting SB’s approval (SB asked me to run any changes that could affect partial charges by him before we allow them into the toolkit). I don’t know the timelines for feedback on that.

Polymer chemical recognition

  • JW – Does this need usage help?

    • CD – Haven’t tried it yet, not sure which project will end up proceeding. Should I give it a shot?

    • JW – Yes, trying it out would be useful on a testing level, and to establish project feasibility.

    • JW – CD could try updating the chemical dictionary (per my message in #developers) to recognize the phosphotyrosine modified amino acid (TPO)

# ACE ALA TPO sidechain ring CO NME mol = Molecule.from_smiles('CC(=O)N[C@H](C)C(=O)N[C@H](Cc1ccc(OP([O-])([O-])(=O))cc1)C(=O)NC') mol.generate_conformers() mol.to_topology().to_file('ALA_TPO.pdb', positions=mol.conformers[0]) mol

 

 

  • OM – I’m planning to go to CUP. Are you, JW?

  • JW – No, I have a personal conflict.

  • OM – CD, would you want to present a poster at CUP?

    • CD – Sure. Would I want to do more work/get more results before presenting?

      • OM + JW – No, you have plenty of data now.

    • OM – Abstracts are due Sun or Mon.

    • CD – Logistics of travel? What day(s) are it?

      • OM – It’s midweek. Not sure about your travel funding, but MS could probably handle it.

      • CD – I’ll check if I have exams/conflicts.

“Here’s the prevalence of connectivity rearrangements in AM1 and they’re easy to detect if you care to look”

“OpenEye uses constrained minimization, but we can’t implement it elsewhere so we just do maxcyc=0, here’s how different the results are”

“Here’s how important ELF conformer selection is for CONSISTENCY BETWEEN DIFFERENT PIPELINES, even if the quality isn’t improved at all”

“Sometimes antechamber and QuacPac apply different BCCs and we don’t know why” (maybe don’t make a big deal about this?)

  • CD will register for CUP and draft an abstract, sending to OM and JW for review. If there’s any trouble with academics/classes then CD will drop out of CUP.

  • OM will contact MS to inform that CD is applying to CUP and determine reimbursement

 

 

 Action items

 Decisions