DOI: 10.5281/zenodo.13757998
title: Simulation data on ORF6 from SARS-CoV-2 for a PhD thesis submitted to University College London

description: Unpublished data from a thesis submitted to University College London in September 2024 

Thesis title: Biophysical characterisation of ORF6 from SARS-CoV-2

Chapter 5 - full-length ORF6 metadynamic simulations in the AMBER03ws force field 

The `Metadynamic_ORF6_full_length_simulations_Zenodo.tar.xz` directory contains data for a 61-residue disordered protein. The protein is ORF6 from SARS-CoV-2. The data were produced by metadynamics simulations in the AMBER03ws force field.  I used PLUMED version 2.7.1 and GROMCS 2021.2. All the data and PLUMED input files required to reproduce the simulation results are available on PLUMED-NEST. This data should be used with the code provided on GitHub at [`https://github.com/alicejpettitt/thesis_2024/tree/main/chapter_5/full-length_orf6`](https://github.com/alicejpettitt/thesis_2024/tree/main/chapter_5/full-length_orf6)

Once downloaded, this directory should be extracted using the following command: 

tar -xzvf Metadynamic_ORF6_full_length_simulations_Zenodo.tar.xz

The directory should be saved with the name `Metadynamic_ORF6_full_length_simulations_Zenodo.tar.xz`` and placed in the same directory as the GitHub `README_metadynamic_simulations.md` file. 

This dataset contains: 



 .pdb - atomic coordinate files for full-length ORF6 in the a03ws force field.

_traj.trr - single concatenated trajectory files for the a03ws (ctr is just the last 21 residues of the full-length simulation).

_weights_corr.dat - weights for each frame in _traj.trr for the a03ws run. Here, the weights of frames in which the peptide interacts with its periodic image have been set to zero. The cutoff was 1.2 nm.

top_frames_.npy - numpy array of frames index for the a03ws simulations. Frames were selected based on weights_corr.dat.

top_frames_.trr - trajectory of frames for the a03ws. Frames were selected based on weights_corr.dat

CS_COLVAR_{system} - experimental and CamShift predicted chemical shifts for the last 21-residues of the full-length ORF6 simulation. 

Contacts directory: Contains Coulomb and LJ input files to make the contact maps.  


Chapter 5 - ORF6-RAE1-NUP98_GLEBS metadynamic simulations in the AMBER99SB-disp force field 

The `Metadynamic_ORF6_complex_simulations_Zenodo.tar.xz` directory contains data for the RAE1-NUP98-ORF6 complex. This was built upon the crystal structure: [`https://www.rcsb.org/structure/7VPH`](https://www.rcsb.org/structure/7VPH). The data were produced by metadynamics simulations in the AMBER99SB-disp force field.  I used PLUMED version 2.7.1 and GROMCS 2021.2. This data should be used with the code provided on GitHub at [`https://github.com/alicejpettitt/thesis_2024/tree/main/chapter_5/orf6-rae1-nup98`](https://github.com/alicejpettitt/thesis_2024/tree/main/chapter_5/orf6-rae1-nup98)

Once downloaded, this directory should be extracted using the following command: 

tar -xzvf Metadynamic_ORF6_complex_simulations_Zenodo.tar.xz

This dataset contains: 



.pdb - atomic coordinate files for the complex in the AMBER99SB-disp force field

traj.trr - single concatenated trajectory files for the

_weights_corr.dat - weights for each frame in _traj.trr for the AMBER99SB-disp force field. Here, the weights of frames in which the peptide interacts with its periodic image have been set to zero. The cutoff was 1.2 nm. weights.dat is before this process.

COLVAR files 


128 starting conformations (gro) files for each system listed above.