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Item | Presenter | Notes |
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Cap library charges | Chapin Cavender | MS: shows slight downside of LibraryCharges in that there should be charge bleeding from caps CC: AMBER RESP charges and CHARMM charges also enforce caps summing to zero – seems necessary unless caps always come in pairs
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Fits with Amber charges | Chapin Cavender | JW: I was under the impression that ff14sb performed best with tip3p Null 0.0.3 OPC3 does keep GB3 stabilized but does not fold 15-mer LS: I’m excited that Null 0.0.3 + OPC passes all tests except the 15-mer CC: Specific 0.0.3 folds 15-mer with all 4 water models on slide 18. But GB3 helix still destabilized CC: we had wanted a force field to pass both the 15-mer and GB3 benchmarks before starting the next step. Is that still the case? MS: most single helices aren’t super stable – is a single alpha helical peptide too stringent a criterion? CC: I think for this temperature (274 K), it’s roughly 50% helix and comparing the chemical shift not too stringent
MS: previously mentioned using a different library of conformers …? (~34 min) CC: should we keep probing Null 0.0.3 + OPC AF: not a lot of man hours, can do a check after a couple microseconds DLM: if we can get a FF that works well with a 4 point water model vs spending more years on a 3 point one, I’d choose the first. We can hedge our bets here. Consensus: keep running other folded proteins while CC continues other pathways of investigation JW: do you have feelings about showing an in-progress protein FF at the annual meeting? We’re doing a tech demo and could feature it with warnings CC: it depends. Not enthusiastic if it causes too much excitement CC: a positive outcome is that it could demonstrate that we are closer to our goal from last year DLM: we should put this in the annual report JW: ok, won’t present live progress on protein FF
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