Ion Parameters
For a full list and explanation of different ion parameters, please see Chapter 3.6 of the Amber Reference Manual.
Choosing Ion Parameters
Choosing parameters for ions can be tricky. Just like each type of biomolecule, each ion (Na+, K+, Mg2+, Cl-, etc. ) will require a set of parameters (lib and frcmod file). Ideally the ions are chosen to be compatible with the water model. Some ions are parameterized against hydration free energies (experimental or TI calculations), ion-oxygen distances and/or lattice energies. You should read each article and understand the pros and cons of each.
12-6 vs. 12-6-4
However ion parameters are chosen, they should be consistent with each other (all 12-6 or all 12-6-4) and the water model. For highly charged metal ions, the 12-6-4 LJ-type nonbonded model performs much better than the 12-6 one overall.
To use the 12-6-4 parameters requires an extra step to insure the C4 term is implemented. One needs to source the leaprc file for the water and then load the 12-6-4 frcmod file by itself, and then use ParmEd to add the C4 terms.
To use the 12-6-4 model see Tutorial 2.4 in the 12-6-4 nonbonded section.
Ion Parameter Set Availability and Implementation
Joung and Cheatham1
This consistent set of parameters for alkali halide ions were developed by fitting solvation free energies, radial distribution functions, ion-water interaction energies and crystal lattice energies and lattice constants for non-polarizable spherical ions.Li+,Na+, K+,Rb+,Cs+, F-,Cl-,Br-,I-
Load the ions lib file and matching water-model frcmod file:
| lib file | frcmod file |
|---|---|
| atomic_ions.lib | frcmod.ionsjc_tip3p |
| frcmod.ionsjc_spce | |
| frcmod.ionsjc_tip4pew |
Li and Merz 12-6 Ions2,3
These ion parameters were parameterized against the experimental hydration free energies and/or ion-oxygen distances.Li+,Na+, K+,Rb+,Cs+,Tl+,Cu+,Ag+,NH4+,H3O+, F-,Cl-,Br-,I-
divalent, trivalent and tetravalent also available - see manual
Load the ions lib file and matching water-model frcmod file:
| lib file |
frcmod file |
|---|---|
| atomic_ions.lib | frcmod.ions1lm_126_tip3p |
| frcmod.ions1lm_126_spce | |
| frcmod.ions1lm_126_tip4pew | |
| frcmod.ionslm_126_opc3 | |
| frcmod.ionslm_126_opc | |
| frcmod.ionslm_126_fb3 | |
| frcmod.ionslm_126_fb4 |
Li and Merz 12-6-4
These ion parameters were parameterized against the experimental hydration free energies and/or ion-oxygen distances. The parameters listed below contain an added r-4 term and reproduce the experimental hydration free energy (HFE), ion-oxygen distand (IOD) and coordination number (CN) values without significant compromise.
To add the C4 term, see Tutorial 2.4 in the 12-6-4 nonbonded section.
Monvalent Ions4,5
Li+,Na+, K+, Rb+, Cs+, Tl+, Cu+, Ag+, NH4+, H3O+, F-, Cl-, Br-, I-
Li+,Na+, K+, Rb+, Cs+, Tl+, Cu+, Ag+, NH4+, H3O+, F-, Cl-, Br-, I-
Load the ions lib file and matching water-model frcmod file:
| lib file |
frcmod file |
|---|---|
| atomic_ions.lib | frcmod.ions1lm_1264_tip3p |
| frcmod.ions1lm_1264_spce | |
| frcmod.ions1lm_1264_tip4pew | |
| frcmod.ionslm_1264_opc3 | |
| frcmod.ionslm_1264_opc | |
| frcmod.ionslm_1264_fb3 | |
| frcmod.ionslm_1264_fb4 |
Divalent Ions6,7
Be2+, Cu2+, Ni2+, Pt2+, Zn2+, Co2+, Pd2+, Ag2+, Cr2+, Fe2+, Mg2+, V2+, Mn2+, Hg2+, Cd2+, Yb2+, Ca2+, Sn2+, Pb2+, Eu2+, Sr2+, Sm2+, Ba2+, Ra2+
Load the ions lib file and matching water-model frcmod file:
| lib file |
frcmod file |
|---|---|
| atomic_ions.lib | frcmod.ions234lm_1264_tip3p |
| frcmod.ions234lm_1264_spce | |
| frcmod.ions234lm_1264_tip4pew | |
| frcmod.ionslm_1264_opc3 | |
| frcmod.ionslm_1264_opc | |
| frcmod.ionslm_1264_fb3 | |
| frcmod.ionslm_1264_fb4 |
Trivalent and Tetravalent Cations8,9
Al3+, Fe3+, Cr3+, In3+, Tl3+, Y3+, La3+, Ce3+, Pr3+, Nd3+, Sm3+, Eu3+, Gd3+, Tb3+, Dy3+, Er3+, Tm3+
Hf4+, Zr4+, Ce4+, U4+, Pu4+, Th4+
Load the ions lib file and matching water-model frcmod file:
| lib file |
frcmod file |
|---|---|
| atomic_ions.lib | frcmod.ions234lm_1264_tip3p |
| frcmod.ions234lm_1264_spce | |
| frcmod.ions234lm_1264_tip4pew | |
| frcmod.ionslm_1264_opc3 | |
| frcmod.ionslm_1264_opc | |
| frcmod.ionslm_1264_fb3 | |
| frcmod.ionslm_1264_fb4 |
Panteva and York Fine-Tuned Divalent Cation Parameters for Nucleic Acids10,11
Mg2+, Mn2+, Zn2+, Cd2+
These 12-6-4 Panteva corrections refer to the fine-tuned C4 terms to be used with TIP4PEW water model and 12-6-4 Li-Merz divalent metal ion parameters with nucleic acids. Fine-tuned parameters exist only for Mg2+, Mn2+, Zn2+ and Cd2+ divalent metal ions.
The corrections are made to the G:N7, A:N7 and :OP atoms, and have to be applied using parmed after the topology and restart files are first generated with the corresponding parameter sets (TIP4PEW water & 12-6-4 Li-Merz divalent metal ions) in leap.
For specific directions on how to use these fine-tuned parameters, please see Example B in Tutorial 2.4 in the 12-6-4 nonbonded section.
Pre-made leaprc files
Note: If wanting to use Joung and Cheatham monovalent cation/anion parameters and Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) one can load the ion parameters and the water model with
OPC water + TIP4PEW ions
leaprc.opc
TIP4PEW water + TIP4PEW ions
leaprc.tip4pew
TIP3P water + Joung/Cheatham K+,Na+,Cl-, Li/Merz Tl+,Cu+, Ag+ NH4+, H3O+, Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set)
leaprc.tip3p
References
1. I.S. Joung and T.E. Cheatham III. Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B, 2008, 112, 9020-9041.2. P. Li; L.F. Song; K.M. Merz, Jr. Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model. J. Chem. Theory Comput., 2015, 11, 1645-1657. Water Model: TIP3P, SPC/E, TIP4PEW.
3. A. Sengupta; Z. Li; L.F. Song; P. Li and K.M. Merz, Jr. Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. J. Chem. Inf. Model., 2021, 61, 869-880.
4. P. Li; L.F. Song; K.M. Merz, Jr. Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model. J. Chem. Theory Comput., 2015, 11, 1645-1657. Monovalent cations and anions for TIP3P, SPCE and TIP4PEW.
5. A. Sengupta; Z. Li; L.F. Song; P. Li and K.M. Merz, Jr. Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. J. Chem. Inf. Model., 2021, 61, 869-880. Monovalent cations and anions for OPC3, OPC, TIP3P-FB, and TIP4P-FB.
6. P. Li and K.M. Merz, Jr. Taking into Account the Ion-Induced Dipole Interaction in the Nonbonded Model of Ions J. Chem. Theory Comput., 2014, 10, 289-297. Divalent cations for TIP3P, SPC/E, and TIP4PEW.
7. Z. Li; L.F. Song; P. Li and K.M. Merz, Jr. Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. J. Chem. Theory Comput, 2020, 16, 4429-4442. Divalent cations for OPC3, OPC, TIP3P-FB, and TIP4P-FB.
8. P. Li; L.F. Song and K.M. Merz, Jr. Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-Type Nonbonded Model in Explicit Water. J. Phys. Chem. B, 2015, 119, 883-895. Trivalent and Tetravalent for TIP3P, SPC/E, and TIP4PEW.
9. Z. Li; L.F. Song; P. Li and K.M. Merz, Jr. Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. J. Chem. Theory Comput., 2021, 17, 2342-2354. Trivalent and Tetravalent for OPC3, OPC, TIP3P-FB, TIP4P-FB.
10. M.T. Panteva; G.M. Giambasu and D.M. York. Comparison of Structural, Thermodynamic, Kinetic and Mass Transport Properties of Mg2+ Ion Models Commonly Used in Biomolecular Simulations. J. Comput. Chem., 2015, 36, 970-982.
11. M.T. Panteva; G.M. Giambasu and D.M. York. Force Field for Mg2+, Mn2+, Zn2+ and Cd2+ Ions That Have Balanced Interactions with Nucleic Acids, J. Phys. Chem. B, 2015, 119, 15460-15470.