This section covers the Aqvist ion parameters as they are implemented into
the towhee_ff_Aqvist file in the ForceFields directory. All of the Towhee atom types for the Aqvist ion force
field are listed, along with a short description of their meanings. This is
not really a comphrehensive stand-alone force field, but is instead a collection
of parameters for the positive ions in the first two columns of the periodic table.
Ion parameters are sometimes hard to come by in the literature so I have included
these parameters for use in conjunction with other force fields (as a simulation of
only positive ions is not very interesting). Note that these are Lennard-Jones (12-6)
parameters and can only be combined with other Lennard-Jones (12-6) force fields.
Any discrepencies (especially typos) from the published Aqvist force field values
are the sole responsibility
of Marcus G. Martin, and I welcome feedback on how this implementation compares
with other programs.
References for Aqvist ions
Aqvist in Towhee
The official force field name for Aqvist ions in Towhee is 'Aqvist'. Here I list all of
the Aqvist atom names for use in the towhee_input file, along with a brief description (although
the meaning of the atom names should be obvious).
Please note that the capitalization and spacing pattern is important
and must be followed exactly as listed here.
- 'Ba+2' : barium ion with a +2 charge
- 'Ca+2' : calcium ion with a +2 charge
- 'Cs+' : cesium ion with a +1 charge
- 'K+' : potasium ion with a +1 charge
- 'Li+' : lithium ion with a +1 charge
- 'Mg+2' : magnesium ion with a +2 charge
- 'Na+' : sodium ion with a +1 charge
- 'Rb+' : rubidium ion with a +1 charge
- 'Sr+2' : strontium ion with a +2 charge
The Aqvist ions utilize point charges. All of the atoms in this force field are ions so the charge assignment
This force field only has parameters for ions so there are no improper torsions.
This force field only has parameters for ions, and while you are welcome to use them with another protein
force field, there are no amino acids in the Aqvist ions force field.
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