| CC Working on following up with stragglers on LiveCOMS review Tried to submit dipeptide dataset on QCFractal on Fri, botched my conda environment, I think I’ve got it fixed so I’ll try again this afternoon Working on getting library charges for protonation states of amino acids. Having trouble with OpenEye. It’s probably from confs that have hbonds on carboxylic acid groups of side chains. JW – Ran into the same thing last week with bespokefit. I’d like to have a way to make it fall back to a nicer behavior if all the carboxylic acid confs are bad. CC – Yeah, I’m trying to think of a manual fix or some other way to handle this. LW – I used rdkit when I did this and didn’t have a problem. I basically used Simon’s ELF code in the toolkit for this. JW – I’ll keep thinking about a general solution for this – Will contact you if I have a fix.
MT General PR wrangling Non-biopolymer non-ParmEd example in toolkit. Found a really odd amber error that causes a memory access error when the number of residues in a prmtop is mis-set. Docs improvements – Users guide, changelog, other fixes. Upstream beta/RC tests. Testing against OpenEye and OpenMM RCs. Already caught an upcoming breaking change OpenMM. Bringing units package to to parity with Evaluator units. Some edge cases, eg OpenMM and SI disagree on what a “dalton” is. Polished and made a new release.
Feedback from protein-ligand example. Mostly requests for improvements in system building experience. Think we’ll need Topology.from_pdb to load multi-protein and water files. MolSSI MMIC proposal. MolSSI recommended that we take the importers and exporters out of interchange and make them MMIC components. I declined this offer. CC – Could you provide details? MT – The project isn’t well adopted and doesn’t have a clear path forward. Getting this tied in with an uncertain effort would be a huge liability for us. JW – Agree. QCFractal appears to be moving forward despite MolSSI, not because of it. I’m worried that MMIC would go the same way. DD – Agree that it’s a big liability to tie ourselves in with something that’s externally developed. If they gain more adoption in the future we can always revisit this.
Started moving stack to M1-compatible builds. Released mdtraj with M1 fixes. We’re still waiting on AmberTools and its dependency chain (parmed is done, packmol seems unmaintained, netcdf-fortran is messy). None of this is super blocking – Rosetta can emulate support for existing packages.
DD LW Worked through nonbonded issues and debugged my dataset with Simon; Simon has updated nonbonded. The entire week spent trying to work directly with evaluator and ForceBalance, as pinning openmm=7.5.1 is not friendly to updated packages Evaluator seems to hang after a few (~3?) hours (no update of progress logs; no increase in file sizes; top shows Python processes with <20% or <10% CPU usage; ps aux shows some generic multiprocessing processes). Stopped at iteration 0 of FB, if properties have been computed, I haven’t found where the output is saved. Tried pushing a few switches, which did not seem to really help: Using DaskLocalBackend (which worked fine for training a force field to 1 property for 15 iterations), with varying numbers of G/CPUs requested Using DaskSlurmBackend, with varying numbers of processes requested Tend to quit jobs after ~24 hours of apparent no progress, so burning a lot of Mobley $
PsiRESP 0.2 is pip installable ( | Github link macro |
|---|
| link | https://github.com/lilyminium/psiresp |
|---|
|
), although RDKit and Psi4 are not. It’s been refactored to use the MolSSI QC stack. Waiting to see if/when QCFractal will patch the issues I’ve raised so I can release 0.2.1 without my own patches – will procrastinate conda recipe until then. Calculates RESP and RESP2 chargesPreviously: CZI meeting very interesting, lots of tips on managing a research project and on being good science citizens (mostly focused on community building). GSOC 2022 will be very different from previous; no longer limited to students but to all new contributors, longer time frame for more flexible hours
PB Submitted the openmm datasets, took longer than expected. Some follow up work related to wbo. Tried looking into torsionnet, they released scripts to train a neural net but not the trained model.
JW –
|