Polarizable MD simulations using AMOEBA Force Field and Monte Carlo Simulations in Python for the study: "Tuning Polyacrylate Composition to Recognize and Modulate Fluorescent Proteins".
f1seq1.xyz, f1seq2.xyz, f8seq1.xyz, pegseq1.xyz - in Tinker XYZ format
parameters.prm, tinker.key
interactionenergy.py - calculates interaction energy between two groups of atoms.
vmd1.tcl - backbone RMSD and radius of gyration (Rg) for GFP; Rg, end-to-end distance, SASA for oligomer;
vmd2.tcl - trans-cis angle for chromophore (CRO)
vmd3.tcl - distance of center of mass (COM) of oligomer from COM of protein and CRO atom 734; coordinates of benzene ring C in CRO
vmd4.tcl - coordinates of imidazole ring atoms in CRO
vmd5.tcl - coordinates of COM of oligomer
vmd6.tcl - RDFs
vmd7.tcl - RMSD of CRO
montecarlo.py - to run the Monte Carlo Simulations
euclideandistance.py - for calculation of Euclidean Distances
If you use this repository or scripts in your work, please cite the associated publication:
Tuning Polyacrylate Composition to Recognize and Modulate Fluorescent Proteins, Darwin C. Gomez, Swarnadeep Seth, Ronnie Mondal, Stephen J. Koehler, Jared G. Baker, Charles Plate, Ian C. Anderson, Mikayla R. Smith, Joey Gloriod, Morgan Gunter, Valerie Vaissier Welborn, Sanket A. Deshmukh, C. Adrian Figg, Angewandte Chemie International Edition, e20032, 2025. doi:10.1002/anie.202520032 Link: https://doi.org/10.1002/anie.202520032