Store Explicit Bonds For AA Residues In PDBxFiles

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Introduction

In the realm of molecular dynamics simulations, storing explicit bonds for amino acid (AA) residues in PDBxFiles is a crucial aspect of accurately representing the molecular structure. The current implementation of creating standard bonds during the createStandardBonds process in OpenMM's PDBFile and PDBxFile reading functions has several limitations and edge cases. In this article, we will explore the proposal of removing the createStandardBonds process and storing explicit bonds for AA residues in PDBxFiles.

The Current Implementation

The current implementation of creating standard bonds during the createStandardBonds process in OpenMM's PDBFile and PDBxFile reading functions has several limitations. The process is used to create bonds between atoms in a molecule, but it has several edge cases, such as multiple protonation states and chain termination. These edge cases make it challenging to accurately represent the molecular structure.

The Proposal

Instead of using the createStandardBonds process, it is proposed that explicit bonds are stored for a Topology's AA residues, at least in PDBxFiles, and possibly in PDB files. This would reduce the complexity of the PDBxFile's reading function, as one would simply iterate over all of the bonds explicitly, gathering orders from some field in a CIF (or pdb CONECT). This approach would also allow for more accurate representation of the molecular structure.

Storing Bond Orders in PDBxFiles

To store bond orders for AA residues in PDBxFiles, one could use the _chem_comp_bond.value_order or the _struct_conn.pdbx_value_order fields in the CIF. These fields are part of the MMCIF dictionary and provide a way to store bond orders in a CIF file.

Why Store Bond Orders in PDBxFiles?

Storing bond orders in PDBxFiles is crucial for several reasons. Firstly, it allows for more accurate representation of the molecular structure. Secondly, it reduces the complexity of the PDBxFile's reading function. Finally, it provides a way to store bond orders in a CIF file, which is a widely used format in molecular dynamics simulations.

Why Not Store Bond Orders in PDB Files?

While storing bond orders in PDB files is also possible, it is not recommended. PDB files are a less well-posed problem than CIF files, and storing bond orders in PDB files would add unnecessary complexity to the PDB file format.

Conclusion

In conclusion, storing explicit bonds for AA residues in PDBxFiles is a crucial aspect of accurately representing the molecular structure. The proposal of removing the createStandardBonds process and storing explicit bonds for AA residues in PDBxFiles is a viable solution to this problem. By storing bond orders in PDBxFiles, we can reduce the complexity of the PDBxFile's reading function and provide a more accurate representation of the molecular structure.

Future Work

Future work on this issue could involve implementing the proposal of storing explicit bonds for AA residues in PDBxFiles. This would involve modifying the PDBxFile reading function to iterate over all of the bonds explicitly, gathering orders from some field in a CIF (or pdb CONECT). Additionally, work could be done to implement the storage of bond orders in PDBxFiles using the _chem_comp_bond.value_order or the _struct_conn.pdbx_value_order fields in the CIF.

Implementation Details

To implement the proposal of storing explicit bonds for AA residues in PDBxFiles, the following steps could be taken:

  1. Modify the PDBxFile reading function to iterate over all of the bonds explicitly.
  2. Gather bond orders from some field in a CIF (or pdb CONECT).
  3. Store bond orders in PDBxFiles using the _chem_comp_bond.value_order or the _struct_conn.pdbx_value_order fields in the CIF.

Code Example

Here is an example of how the modified PDBxFile reading function could be implemented:

void PDBxFileReader::readTopology() {
  // Iterate over all of the bonds explicitly
  for (const auto& bond : topology.getBonds()) {
    // Gather bond orders from some field in a CIF (or pdb CONECT)
    int order = getBondOrder(bond);
    // Store bond orders in PDBxFiles using the `_chem_comp_bond.value_order` or the `_struct_conn.pdbx_value_order` fields in the CIF
    storeBondOrder(bond, order);
  }
}

This code example illustrates how the modified PDBxFile reading function could be implemented to store explicit bonds for AA residues in PDBxFiles.

Conclusion

Q: What is the current implementation of creating standard bonds in OpenMM's PDBFile and PDBxFile reading functions?

A: The current implementation of creating standard bonds during the createStandardBonds process in OpenMM's PDBFile and PDBxFile reading functions has several limitations and edge cases. The process is used to create bonds between atoms in a molecule, but it has several edge cases, such as multiple protonation states and chain termination.

Q: Why is the createStandardBonds process not sufficient for accurately representing the molecular structure?

A: The createStandardBonds process is not sufficient for accurately representing the molecular structure because it has several limitations and edge cases. These limitations and edge cases make it challenging to accurately represent the molecular structure.

Q: What is the proposal for storing explicit bonds for AA residues in PDBxFiles?

A: The proposal is to remove the createStandardBonds process and store explicit bonds for AA residues in PDBxFiles. This would reduce the complexity of the PDBxFile's reading function, as one would simply iterate over all of the bonds explicitly, gathering orders from some field in a CIF (or pdb CONECT).

Q: Why is storing bond orders in PDBxFiles important?

A: Storing bond orders in PDBxFiles is important because it allows for more accurate representation of the molecular structure. It also reduces the complexity of the PDBxFile's reading function and provides a way to store bond orders in a CIF file, which is a widely used format in molecular dynamics simulations.

Q: Why not store bond orders in PDB files?

A: While storing bond orders in PDB files is also possible, it is not recommended. PDB files are a less well-posed problem than CIF files, and storing bond orders in PDB files would add unnecessary complexity to the PDB file format.

Q: How would the modified PDBxFile reading function be implemented?

A: The modified PDBxFile reading function would iterate over all of the bonds explicitly, gather bond orders from some field in a CIF (or pdb CONECT), and store bond orders in PDBxFiles using the _chem_comp_bond.value_order or the _struct_conn.pdbx_value_order fields in the CIF.

Q: What are the benefits of storing explicit bonds for AA residues in PDBxFiles?

A: The benefits of storing explicit bonds for AA residues in PDBxFiles include:

  • More accurate representation of the molecular structure
  • Reduced complexity of the PDBxFile's reading function
  • Ability to store bond orders in a CIF file, which is a widely used format in molecular dynamics simulations

Q: What are the challenges of implementing the proposal of storing explicit bonds for AA residues in PDBxFiles?

A: The challenges of implementing the proposal of storing explicit bonds for AA residues in PDBxFiles include:

  • Modifying the PDBxFile reading function to iterate over all of the bonds explicitly
  • Gathering bond orders from some field in a CIF (or pdb CONECT)
  • Storing bond orders in PDBxFiles using the _chem_comp_bond.value_order or the _struct_conn.pdbx_value_order fields in the CIF

Q: What is the expected outcome of implementing the proposal of storing explicit bonds for AA residues in PDBxFiles?

A: The expected outcome of implementing the proposal of storing explicit bonds for AA residues in PDBxFiles is a more accurate representation of the molecular structure, reduced complexity of the PDBxFile's reading function, and the ability to store bond orders in a CIF file, which is a widely used format in molecular dynamics simulations.

Q: What is the next step in implementing the proposal of storing explicit bonds for AA residues in PDBxFiles?

A: The next step in implementing the proposal of storing explicit bonds for AA residues in PDBxFiles is to modify the PDBxFile reading function to iterate over all of the bonds explicitly, gather bond orders from some field in a CIF (or pdb CONECT), and store bond orders in PDBxFiles using the _chem_comp_bond.value_order or the _struct_conn.pdbx_value_order fields in the CIF.