Do we need to remove HETATM and CONECT records from the `.pdb` file before creating a topology?

[schampoux]

This issue is to address the questions of removing HETATM and CONECT records from the .pdb file before creating a topology. This is an approach that was found in one of the tutorials, and it is noteworthy to understand what its doing to see if we need to apply it to the pipeline or not.

[schampoux]

HETATM: Records/lines in the .pdb file with this label denote atoms that are part of a heterogeneous group, meaning they are not part of the standard amino acid or nucleotide residues that make up proteins and nucleic acids, respectively. This can include:

• water molecules
• metal ions
• other molecules These are bound to the protein or nucleic acid including ligands, inhibitors, cofactors, and other small molecules.

CONECT: Records/lines containing this label specify the connectivity between atoms, indicating which atoms are bonded to which.

• Used to define the bonding relationships between non-standard residues and other molecules within the structure.
• Crucial for accurately representing the structure of heteroatoms and complex bonding simulations that cannot be inferred from standard templates.

Both of these records are essential for a detailed and accurate representation of the molecular structure being described.

Should these records be removed in the pipeline? This implies all .pdb's will be stripped of these records.

Implications of Removal: Simplification = the system is simpler and might run more smoothly in terms of setup, expeciall with automated topology generation tools that may not handle non-standard residues or ligands well. For simulations where non-proteins components play a critical role (e.g., in binding studies or enzymatic reactions), removing these records can result in a loss of essential interactions and functional insights.

• Note: protein folding simulations differ significantly from binding studies or enzymatic reactions in their focus and setup.
  • Protein folding simulations are concerned with how a protein chain folds into its functional three-dimensional structure from an unfolded state. These studies typically focus on the intrinsic properties of the protein itself.
  • Binding studies and enzymatic reactions involve interactions between the protein and one or more external molecules.

Conclusion: For the sake of development, it is safe for us to remove these records in the pipeline. link to the gpt conversation