To begin, download the PDB file of the thioredoxin protein as the model protein system. Use an appropriate protein visualizer software to erase water molecules, dimers, and ligands from the protein structure. Add the file with modified amino acid residues from-lib.
pdb and overlay it on the amino acid residue to be modified. Ensure that the amino and carbonyl ends of from-lib. pdb accurately matches the amino acid intended for modification.
Delete the protein, leaving only the from-lib. pdb file in the three-dimensional space occupied by the amino acid residue to be modified. Remove hydrogen from the N and C-terminal atoms.
Save the from-lib. pdb as u00-moved. pdb with the new coordinates.
Using a text editor, open the cleaned protein PDB file and u00-moved. pdb file. Copy the coordinates from u00-moved.
pdb and paste them into the protein PDB file to adapt the bond between the modified residue and the protein system. Adjust the typology to be compatible with the protein PDB format, changing HEATATM to ATOM and updating the number one to the one corresponding to the residue to be modified. Save the new file as complex.pdb.
Structures from density functional theory at m062x/631g level compared with AMBER's molecular dynamics simulations correlated well with theoretical quantum mechanics, showing minimal bond distance errors and angle parameter values. The RMSD values obtained for each of the modified amino acids were similar to native counterparts and maintained confirmational stability throughout the entire trajectory.
