/
2020-03-27 Cerutti Onboarding

2020-03-27 Cerutti Onboarding

Owned by Jeffrey Wagner
Last updated: Mar 28, 2020 by David Cerutti (Deactivated)
1 min read

Date

Mar 27, 2020

Participants

  • @Jeffrey Wagner

  • @David Cerutti (Deactivated)

Discussion topics

Item

Notes

Item

Notes

General onboarding checklist https://openforcefield.atlassian.net/wiki/spaces/OFFO/pages/62324786

  • Done

Walk through smirnoff99Frosst repo structure

  • FF14SB repo could use this as a template

  • https://github.com/openforcefield/smirnoff99Frosst/

    • Releases:

    • Release process:

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"

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

https://open-forcefield-toolkit.readthedocs.io/en/latest/smirnoff.html#librarycharges-library-charges-for-polymeric-residues-and-special-solvent-models

<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>

Result posted to slack: https://openforcefieldgroup.slack.com/archives/C4VHEFXS5/p1585337569000600?thread_ts=1575750481.078600&cid=C4VHEFXS5

 

 

Action items

@David Cerutti (Deactivated) will send a headshot for the website to @Karmen Condic-Jurkic

Decisions