This repo contains the data from: EVCouplings, DynaMut2, MDM-TASK, MD simulation.
For PBC correction (1 Protein and 0 System)
echo 1, 0 |gmx trjconv -s md.tpr -f md.xtc -o md_corr.xtc -center -ur compact -pbc mol
Visualization in VMD
PBC Correction:
vmd step3_input.psf md_corr.xtc
Protein Alignment:
VMD Main > Extension > Analysis > RMSD Trajectory Tool > Align (using protein) > RMSD
VMD Main > Graphics > Representations > index 0 to 26513 (in Selection Atoms Panel) > Enter
Save Protein-Nucleic Acid Complex in .dcd format:
VMD Main > File > Save Coordinates > Selected Atoms: index 0 to 26513 > File Type: dcd > Save > Protein_NA_complex.dcd
VMD Main > File > Save Coordinates > Selected Atoms: index 0 to 26513 > File Type: pdb > Frames: First 0, Last 0, Stride, 1 > Save > Protein_NA_complex.pdb
Visualizing Protein-Nucleic Acid Complex:
vmd Protein_NA_complex.pdb Protein_NA_complex.dcd