Add example of stitching NAGL charges into ff14SB + Sage #7
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nagl-biopolymer/run.py
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| print("replacing dummy charges with NAGL charges ... ") | ||
| for key, charge in interchange["Electrostatics"].charges.items(): | ||
| if charge.m == 0.0: |
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(not blocking) It'd be better if this were handled by checking the parameter ID instead of the numerical value. I'm not sure whether there are any 0-charge atoms in ff14SB but if we extend this workflow to other FFs this may become important.
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Nice catch, the housekeeping here was difficult for me to think through at first
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| print(f"total system charge is {get_total_charge(simulation.system)}") |
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(blocking) We'll need to be able to handle really weird PTMs that withdraw/donate partial charge from/to neighboring residues. So some form of normalization will be needed in this workflow, but it should never change atoms whose charge was assigned by ff14sb. A minimal approach would be to normalize any nonintegral charges over all NAGL-assigned atoms. And an improvement on that would be to normalize within contiguous groups of NAGL-assigned atoms.
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Fair enough; in the spirit of "anything goes" I'm going with the simple approach. I think a more thorough charge normalization routine would require a decent amount of application-specific details that I don't want to implement here without some more consideration; it seems like the sort of feature that would be broadly useful to users of the toolkit who care about biopolymers so I'd like to see it upstreamed
With a really quick 1 minute simulation (9.3 ps) run locally, the simulation doesn't immediately unravel