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Research data supporting: "Conformational Energy Landscape of the Ritonavir Molecule"

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Chakraborty, Debayan 
Sengupta, Neelanjana 
Wales, David J. 


pathsample: This directory contains the converged stationary point databases for ritonavir which were used for the rate calculations, as well as the generation of the disconnectivity graphs. The Intel Fortran compiler, version 13.1 (64 bit) was used to compile OPTIM and PATHSAMPLE. (1) -> database of minima (2) -> database of transition states (3) points.min -> structures of all the minima in the database. (4) points.ts -> structures of all the transition states in the database. (5) odata.connect -> Input file for running OPTIM connections (6) pathdata -> PATHSAMPLE input file (7) coords.prmtop -> AMBER topology file (8) coords.inpcrd -> AMBER coordinate file (9) -> AMBER specific input file for computing single point energies (10) min.A -> cis (form II) conformation (11) min.B -> trans (form I) conformation. (12) EofS -> The profile for the fastest path between the cis and trans polymorphs. Running PATHSAMPLE with the current keywords will compute the rate constant for cis <-> trans conformational transition, at a regrouping threshold of 3.0 kcal/mol and temperature of 298 K (0.592 in units of kcal/mol). For sampling specific keywords please refer to the PATHSAMPLE and OPTIM user manuals. (See and For further queries please email Prof David J. Wales ( optim_gaussian_input: This directory contains the relevant input files for reoptimising the transition state using DFT at the B3LYP/6-31G(d) level using Gaussian 03 interfaced to the OPTIM code. (1) odata.g03.ts -> OPTIM input file for reoptimisation of the transition state structure. (2) odata.g03.path -> OPTIM input file for finding out the minima connected to the DFT transition state. (3) -> atom names in the order they appear in the pdb/xyz files. (4) gaussian.inp.pre -> information regarding the functional and basis sets used. OPTIM requires this file to create a Gaussian input on the fly. structures: This directory contains the structures that were reoptimised with DFT. They are in a format suitable for OPTIM calculations. These structures correspond to minima which are connected to at least two transition states and lie below monotonic sequences. gaussian_files: This directory contains subdirectories corresponding to each structure that was reoptimised with DFT. Within each subdirectory, the relevant input and output files can be found.


Software / Usage instructions

The data has been zipped into a .zip format, and should open with any unzipping tool. All the files within the directories are in plain text format, and should open with any text editor. The points.min and points.ts files are in binary format.


ritonavir, energy landscape, discrete path sampling


University of Cambridge
This work was supported by the ERC [grant number MAAG/837 RG59508].