Date
Participants
Discussion topics
Item | Notes |
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General onboarding checklist Joining the team |
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Walk through smirnoff99Frosst repo structure |
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Reproduce a fit using ForceBalance | Tutorial for fitting in README here: Miniconda install instructions: wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh bash ./Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda3 source ~/miniconda3/etc/profile.d/conda.sh Forcebalance install instructions conda create -n fb-fit -c conda-forge -c omnia -c openeye geometric openeye-toolkits forcebalance openforcefield Confirm OE install >>> from openeye import oechem >>> mol = oechem.OEMol() Install workqueue wget https://raw.githubusercontent.com/leeping/forcebalance/master/tools/install-cctools.sh bash install-cctools.sh echo "Checking for Work Queue import; if successful, no message will be printed" python -c "import work_queue" export PATH="$HOME/opt/cctools/current/bin:$PATH"
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Making a development build of OFF Toolkit | conda create -n off-dev -c conda-forge -c omnia -c openeye openforcefield openeye-toolkits conda activate off-dev conda remove --force openforcefield pip install -e . |
Walk through FF API | |
Build workflow to compare librarycharges between AmberTools-parametrized ALA and SMIRNOFF-parametrized ALA | <LibraryCharges version="0.3"> <!-- match a non-terminal alanine residue with AMBER ff14SB partial charges --> <LibraryCharge name="ALA" smirks="[NX3:1]([#1:2])([#6])[#6H1:3]([#1:4])([#6:5]([#1:6])([#1:7])[#1:8])[#6:9](=[#8:10])[#7]" charge1="-0.4157*elementary_charge" charge2="0.2719*elementary_charge" charge3="0.0337*elementary_charge" charge4="0.0823*elementary_charge" charge5="-0.1825*elementary_charge" charge6="0.0603*elementary_charge" charge7="0.0603*elementary_charge" charge8="0.0603*elementary_charge" charge9="0.5973*elementary_charge" charge10="-0.5679*elementary_charge"/> </LibraryCharges> |
Action items
- David Cerutti (Deactivated) will send a headshot for the website to Karmen Condic-Jurkic
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