Ion Modeling using Nonbonded Model

Ion recognition in leap

The nonbonded model treats the metal ion as a particle which only has nonbonded interactions (such as electrostatic and VDW interactions) with surrounding molecules. The charge of the ion is an integer number representing its oxidation state. In the Amber force field, there are only two parameters needed for the 12-6 Lennard-Jones (LJ) nonbonded model of ions: charge and LJ parameters while for the 12-6-4 nonbonded model there is one additional C₄ term which can be added using ParmEd. The atomic_ions.lib file in the $AMBERHOME/dat/leap/lib/ directory was used to define the charges and atom types of the different kinds of atomic ions for the nonbonded model. To make things clear, users can check the atomic_ions.cmd file (also in the $AMBERHOME/dat/leap/lib/ directory) because it is used to generate the atomic_ions.lib file. Generally, in the AMBER force field, the atomic ion has its atom type equal to its element plus its charge. For example, the sodium ion has atom type as Na+, chloride ion has atom type Cl-, magnesium ion has the atom type Mg2+, zinc ion has the atom type Zn2+, while the ferric iron ion has atom type Fe3+ and so on (this is different than the atom type used for ions in the bonded model, where the ion should have an atom type with only two letters). Here we treat the zinc ion as an example to show how the atomic ion is recognized in leap program.

In PDB files ions are usually treated as "HETATM":

HETATM 4307 ZN ZN A1612 3.200 15.868 15.157 0.50 15.29 ZN

You can find three "ZN" symbols (in the 3rd, 4th and last columns) in this line but they have different meanings. The line means there is an atom ZN (3rd column) in residue ZN (4th column) and its element is ZN (last column).

If you check the atomic_ion.cmd file, you find the following lines (with our added explanations after each line):

i = createAtom ZN Zn2+ 2.0 #Create an atom i with atom name ZN, atom type Zn2+ and charge 2.0 set i element "Zn" #Set element of atom i as Zn set i position { 0 0 0 } #Set coordinates of atom i as {0, 0, 0} r = createResidue ZN #Create a residue r with residue name ZN add r i #Add the atom i into residue r ZN = createUnit ZN #Create a unit ZN with unit name ZN add ZN r #Add the residue r into unit ZN saveOff ZN ./atomic_ions.lib #Save information of unit ZN into atomic_ions.lib file

After running these commands using leap (you can add these lines into a input file and use tleap -s -f input_file to do that), a unit named ZN, which includes a residue named ZN that contains an atom named ZN with atom type Zn2+ and 2.0 charge, will be stored in the library file atomic_ions.lib.

If you use the "loadoff atomic_ions.lib" command in leap and then load a PDB file containing Zn ion(s) which has the format shown above, leap will recognize the ZN ion(s) automatically (because of the match of the residue and atom names between the PDB file and the library file) and assign a charge of 2.0 and an atom type Zn2+ to the Zn ion(s).

Afterwards you need to load the LJ parameters for the Zn2+ atom type. There are various parameter files, which represent different parameter sets, available in the $AMBERHOME/dat/leap/ directory. The explanation of related files is found in Amber force fields-->Molecular mechanics force fields-->Ions section.

In the current version most of the ions (but not all) available in atomic_ions.lib file are compatible with the PDB naming scheme. If it doesn't meet your needs, you can create a library file yourself according to the style shown above and load it in leap for charge and atom type assignment to the ion(s).

Click here to go to: Example of using 12-6 Nonbonded model

Click here to go to: Example of using 12-6-4 LJ-Type Nonbonded model

Click here to go to: Example of using modified 12-6-4 LJ-Type NB model