PBRadii

Warning

Please, note that this section is in active development; thus some elements could change in future versions

Introduction¶

Previous results suggest that the PB/GB predictions are largely impacted by the radii used, as the multiple variants of radii give very different results (check Wang et. al., 2019 for an extensive review on this and other factors). In our interest in providing the users with all available tools, we have implemented 10 radii sets available in the literature that you can define with the PBRadii variable in the input file:

Radii Name	Type	FF Compatibility	Compatibility
`amber6`	`atom_number`+`bonded_atom_number`	any, but optimized for Amber	generic
`bondi`	`atom_number`	any, but optimized for Amber	generic
`mbondi`	`atom_number`+`bonded_atom_number`	any, but optimized for Amber	generic
`mbondi2`	`atom_number`+`bonded_atom_number`	any, but optimized for Amber	generic
`mbondi3`	`atom_number`+`bonded_atom_number`+`residue`	any, but optimized for Amber	generic
`mbondi_pb2`	`atom_number`+`bonded_atom_number`	any, but optimized for Amber	generic
`mbondi_pb3`	`atom_number`+`bonded_atom_number`	any, but optimized for Amber	generic
`charmm_radii`	`charmm_radii`	charmm	complete
`tyl06`	`residue`	amber (optimized), charmm (experimental)	semi-complete
`yamagishi`	`residue`	amber (optimized), charmm (experimental)	semi-complete

Radii file structure¶

The radii data is contained in a JSON format file. It is a dictionary (key-value pair) that contains all the required information. The most important keys are forcefield, type, and radii, so please, pay attention to them when modifying or generating a new radii set. This format is extremely versatile and allows adding new atoms or modifying the current ones:

mbondi radii

{
  "name": "mbondi",
  "forcefield": ["all"],   // (1)!
  "implementation": "xBFreE Team",
  "RADIUS_SET": "modified Bondi radii (mbondi)",
  "reviews": [],
  "reference": "",
  "notes": "",
  "type": "atom_number+bonded_atom_number",   // (2)!
  "radii": [   // (3)!
    {"atom_number": 1 , "atom_type": null, "bonded_atom_number": 6 , "mass": null, "radii": 1.3 },
    {"atom_number": 1 , "atom_type": null, "bonded_atom_number": 7 , "mass": null, "radii": 1.3 },
    {"atom_number": 1 , "atom_type": null, "bonded_atom_number": 8 , "mass": null, "radii": 0.8 },
    {"atom_number": 1 , "atom_type": null, "bonded_atom_number": 16, "mass": null, "radii": 0.8 },
    {"atom_number": 1 , "atom_type": null, "bonded_atom_number": null, "mass": null, "radii": 1.2 },
    {"atom_number": 6 , "atom_type": "^C1", "bonded_atom_number": null, "mass": ">13.0", "radii": 2.2 },
    {"atom_number": 6 , "atom_type": "^C2", "bonded_atom_number": null, "mass": ">14.0", "radii": 2.2 },
    {"atom_number": 6 , "atom_type": "^C3", "bonded_atom_number": null, "mass": ">15.0", "radii": 2.2 },
    {"atom_number": 6 , "atom_type": null, "bonded_atom_number": null, "mass": null, "radii": 1.7 },
    {"atom_number": 7 , "atom_type": null, "bonded_atom_number": null, "mass": null, "radii": 1.55},
    {"atom_number": 8 , "atom_type": null, "bonded_atom_number": null, "mass": null, "radii": 1.5 },
    {"atom_number": 9 , "atom_type": null, "bonded_atom_number": null, "mass": null, "radii": 1.5 },
    {"atom_number": 14, "atom_type": null, "bonded_atom_number": null, "mass": null, "radii": 2.1 },
    {"atom_number": 15, "atom_type": null, "bonded_atom_number": null, "mass": null, "radii": 1.85},
    {"atom_number": 16, "atom_type": null, "bonded_atom_number": null, "mass": null, "radii": 1.8 },
    {"atom_number": 17, "atom_type": null, "bonded_atom_number": null, "mass": null, "radii": 1.7 },
    {"atom_number": "*", "atom_type": null, "bonded_atom_number": null, "mass": null, "radii": 1.5 }
  ]
}

Please, pay attention to this key when modifying or generating new radii set
Please, pay attention to this key when modifying or generating new radii set
Please, pay attention to this key when modifying or generating new radii set

The content of the key radii corresponds to the conditions for assigning the value of radii per atom. As seen in the Type column of the table above, there are various combinations depending on the selected radii set.

Understanding the radii classification/type¶

In the table above, the Type column shows several combinations. Each keyword is used as a condition to assign the radii to any atom. Let's analyze the previous example: mbondi In this case, a combination of atom_number and bonded_atom_number is highlighted.

Why not include atom_type or mass?

The atom_type keyword is included in all generic defined radii, so it would be redundant to define it. On the other hand, mass is evaluated for all radii set based on atom_number (all except charmm_radii, tyl06 and yamagishi)

Here we first check the atom_number, then if atom_type and mass or bonded_atom_number were defined. If the processed atom meets the conditions, it is assigned the specific defined value, otherwise, it is assigned a generic value defined in the file with atom_number="*"

Simple case to add a new atom parameter¶

Suppose you want to add a new atom parameter, for example, iron (Fe). For this, you must copy the radii base file (for example, mbondi) and add the new data as follows:

modified mbondi radii

{
  "name": "new-mbondi",    // (1)!
  "forcefield": ["all"],   
  "implementation": "Me",  // (2)!
  "RADIUS_SET": "modified Bondi radii (mbondi) for Fe",
  "reviews": [],
  "reference": "",
  "notes": "I have added the Fe parameters",    // (3)!
  "type": "atom_number+bonded_atom_number",   // (4)!
  "radii": [   
    {"atom_number": 1 , "atom_type": null, "bonded_atom_number": 6 , "mass": null, "radii": 1.3 },
    {"atom_number": 1 , "atom_type": null, "bonded_atom_number": 7 , "mass": null, "radii": 1.3 },
    {"atom_number": 1 , "atom_type": null, "bonded_atom_number": 8 , "mass": null, "radii": 0.8 },
    {"atom_number": 1 , "atom_type": null, "bonded_atom_number": 16, "mass": null, "radii": 0.8 },
    ...
    {"atom_number": 17, "atom_type": null, "bonded_atom_number": null, "mass": null, "radii": 1.7 },
    {"atom_number": 26, "atom_type": null, "bonded_atom_number": null, "mass": null, "radii": 1.6 }, // (5)!
    {"atom_number": "*", "atom_type": null, "bonded_atom_number": null, "mass": null, "radii": 1.5 }
  ]
}

New name
author
Author's notes
Please, take care your modifications and the type
Note that we add the new atom parameters before the "atom_number": "*"

Now, this new file can be defined as the radii in the variable PBRadii, for example:

Sample input file for GB calculation

&general
  PBRadii = /home/user/path/to/new_radii.json 
/

&gb
igb=5, saltcon=0.150,
/

Create, test, and share your radii

This feature is experimental, so we need to test it in a broader scenario. If you find a bug, please report it. You will receive due credit in the "reviews" section of the radii archive.
If you create or optimize your radii, feel free to share it, and we will include it in the list of radii.
We don't show much information about the radii used at this time, but we plan to have it displayed in the output file.

2023-07-17 2023-05-27