choderalab/nanoparticles

Scripts to set-up and run simulations composed of mixtures of insoluble molecules and dye.

nanoparticles

Scripts and files for nanoparticle simulations.

Manifest

name_list.txt:   the naming scheme of the molecules and simulations.

ImplicitAssembly

Scripts and structures from the assembly of nanoparticles in implicit solvent.

ExplicitProduction

Unbiased molecular dynamics of the model nanoparticles that were created in implicit solvent

AnalysisTools

Python scripts for nanoparticle analysis.

OriginalFiles/

    The original mol2 files of drugs and dye molecules sent to Gregory Ross by Yosef Shamay.

CleanedFiles/

    Mol2 files from OriginalFiles/ given cleaner names and ligand residue names given.

ParamFiles/

    Mol2 files from CleanedFiles parameterised with antechamber and parmchk.
    Imprecision in Ambermini's sqm code results in molecules with (slightly) non unit charge.
    This procedure will be replaced with parameteriztion with OpenEye from Openmoltools.

GrantFigures

Figures produced for the collaborative grant with the Heller Lab.