Use 12-6-4 LJ potential for Divalent/Trivalent ions in AMBER.

My advisor had plan to use divalent salts in the project. I checked some literatures and found AMBER14 had better solution for that.

AMBER14 supplied a set of parameters for monovalent, divalent and trivalent ions. Please check the manual, in AMBERTOOLS15, it located at page 45 “3.9 Ions”. You may read the detail for more information.

AMBER14 could use 12-6-4 LJ potential to replace the conventional 12-6 LJ potential to take into account the charge induced dipole interaction by multivalent ions. Simulation results fit with experimental data very well ( hydration free energies, ion-water distance and coordinate number). Previously, with 12-6 LJ potential, simulation results can not fit all the experimental data at the same time. The improved LJ potential can solve this problem. You may check the citation to know more about the development of the 12-6-4 LJ potential (Li, P.; Merz, K. Jr. Taking into Account the Ion-Induced Dipole Interaction in the Nonbonded Model of Ions. J. Chem. Theory Comput., 2014, 10, 289–297.)

I write a tleap script here for how to build a water box later.

First, you need to know if your salts are included in AMBER14. Please check $AMBERHOME/dat/leap/lib/atomic_ions.cmd, and remember the residue name for each ion.

Second, load the ions parameters. Here I choose TIP3P water model.

Third, generate the PRMTOP and INPCRD files.

Fourth, modify the PRMTOP to use 12-6-4 LJ potential equation by

Fifth, tell sander to use 12-6-4 LJ potential for the simulation.

The script for tleap to generate PRMTOP and INPCRD is below. The salt is CaCl2. CA is Ca2+; CL is Cl-.

source leaprc.ff14SB
loadOff atomic_ions.lib #residue name for ions
loadamberparams frcmod.ions1lsm_1264_tip3p #monovalent ions 
loadamberparams frcmod.ionslm_1264_tip3p #divalent ions
loadamberparams frcmod.ions34lsm_1264_tip3p #trivalent ions
i = loadpdb test.pdb
check i
solvatebox i TIP3PBOX 10 0.75
addions i CA 10 CL 20
charge i
saveamberparm i test_CaCl2.prmtop test_CaCl2.inpcrd

The command to modify PRMTOP file is below. The following is not a script. You may see the information to modify the 12-6-4 LJ potential. The water model need to be specified, TIP3P is the default option. You may check the modified.prmtop and an additional LENNARD_JONES_CCOEF at the end of the file. test_CaCl2.prmtop
>add12_6_4 :CA,CL
Adding Lennard-Jones C-coefficient for 12-6-4 potential. Polarizabilities read from [$AMBERHOME/dat/leap/parm/lj_1264_pol.dat]. Using default C4 parameters for water model [TIP3P].
The selected metal ion is Ca
The selected metal ion is Cl
>outparm modified.prmtop

Add lj1264=1 in your input file for simulation.

This feature is now only available for CPU computing with SANDER or PMEMD. GPU computing can not use it.


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