Page Comparison

...

• Download/load in crystal structures for COD

  • Some code about parsing the COD using rdkit: https://pschmidtke.github.io/blog/rdkit/crystallography/small%20molecule%20xray/xray/database/2021/01/25/cod-and-torsion-angles.html .

• Convert crystals into formats that OpenFF can use:

  • To get CIF into OpenFF, see PyCIFRW (https://github.com/openforcefield/openff-toolkit/pull/982/files )

  • Open Eye toolkit can also load CIF files: https://docs.eyesopen.com/toolkits/python/oechemtk/OEChemConstants/OEIFlavor.html?highlight=cif#OEChem::OEIFlavor::CIF

  • Use openBabel to convert CIF to pdb file and generate openFF Molecule object with pdb + SMILES string

  • Use PyMol to generate an appropriate unit cell and supercell based on crystal symmetry information in cif/pdb files. Use supercell to generate openMM topology.

• Select structures from COF:

  • For now, just take structures that are organic crystals and not weird. Eventually, we will want to figure these out.

  • Can start by just selecting a few (5-10) COF files to get the process working.

  • COF has SMILES database, but some stereochemistries are not explicitly defined, which will cause errors when generating openFF molecule.

• Minimize the structures using different force fields:

  • Start with OpenFF (different versions)

  • Example here:

    Github link macro
    link https://github.com/openforcefield/openff-toolkit/tree/latest/examples/SMIRNOFF_simulation

    could be used to start with (energy minimize rather than simulate)

  • Issue: we may need to do lattice minimization (minimize the box vectors as well as the atoms), which will require implementing some code.

  • Will need to minimize unit cells as well. Many programs implement this, we should figure out the best algorithms:

    • http://tutorials.crystalsolutions.eu/tutorial.html?td=optgeom&tf=opt_tut#geopin

    • https://dasher.wustl.edu/tinker/downloads/tinker-guide.pdf

    • https://www.scm.com/doc/Tutorials/ExternalPrograms/QEGeometryOptimization.html

    • Basically, one needs to minimize in 3*natoms + 6 variables (box vectors).

      • Use any optimization routine (in scipy?) and calculate the derivatives as follows:

        • For coordianate derivitives, calculate the force from OpenMM

        • for box vector derivatives, pick a spacing “esp”, and increase/decrease the box vectors by “esp” by calling the OpenMM energies, then calculate the finite difference derivative. Eps should probably be around 0.001 relative of the variable.

• Observe how much the RMSD changes from the experimental structure.

  • Note: there are other more direct comparisons to experiment (see below), but let’s get the other things working first

  • Look at RMSD20 and RMSD15

• Goals: make it a workflow that can run relatively easily and be plugged into benchmarking

  • Will synchronize with Simon Boothroyd once the basic version is working.

...