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custom_ions_menu.yml
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custom_ions_menu.yml
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martini:
cations:
CA:
atoms: [CA]
abbr: CA
base: dry_martini_v2.1.rtf
charge: 2
name: Ca<sup>2+</sup>
K:
atoms: [K]
abbr: K
base: dry_martini_v2.1.rtf
charge: 1
name: Cl<sup>+</sup>
NA:
atoms: [NA]
abbr: NA
base: martini_v2.0_ions.rtf
charge: 1
name: Cl<sup>+</sup>
NC3:
atoms: [NC3]
abbr: NC3
base: martini_v2.0_ions.rtf
charge: 1
name: Choline
anions:
CL:
atoms: [CL]
abbr: CL
base: martini_v2.0_ions.rtf
charge: -1
name: Cl<sup>-</sup>
charmm:
cations:
title: Cation Type
sub:
alkali_metals:
title: Alkali Metals
sub:
LIT:
atoms: [LIT]
abbr: Li
base: toppar_water_ions.str
charge: 1
name: Li<sup>+</sup>
SOD:
atoms: [SOD]
abbr: Na
base: toppar_water_ions.str
charge: 1
name: Na<sup>+</sup>
POT:
atoms: [POT]
abbr: K
base: toppar_water_ions.str
charge: 1
name: K<sup>+</sup>
RUB:
atoms: [RUB]
abbr: Rb
base: toppar_water_ions.str
charge: 1
name: Rb<sup>+</sup>
CES:
atoms: [CES]
abbr: Cs
base: toppar_water_ions.str
charge: 1
name: Cs<sup>+</sup>
alkaline_earth_metals:
title: Alkaline Earth Metals
sub:
BE2P:
atoms: [BE2P]
abbr: Be
base: toppar_ions_won.str
charge: 2
name: Be<sup>2+</sup>
MG:
atoms: [MG]
abbr: Mg
base: toppar_water_ions.str
charge: 2
name: Mg<sup>2+</sup>
CAL:
atoms: [CAL]
abbr: Ca
base: toppar_water_ions.str
charge: 2
name: Ca<sup>2+</sup>
SR2P:
atoms: [SR2P]
abbr: Sr
base: toppar_ions_won.str
charge: 2
name: Sr<sup>2+</sup>
BAR:
atoms: [BAR]
abbr: Ba
base: toppar_water_ions.str
charge: 2
name: Ba<sup>2+</sup>
RA2P:
atoms: [RA2P]
abbr: Ra
base: toppar_ions_won.str
charge: 2
name: Ra<sup>2+</sup>
transition_metals:
title: Transition Metals
sub:
AG1P:
atoms: [AG1P]
abbr: Ag
base: toppar_ions_won.str
charge: 1
name: Ag<sup>+</sup>
AG2P:
atoms: [AG2P]
abbr: Ag
base: toppar_ions_won.str
charge: 2
name: Ag<sup>2+</sup>
AU1P:
atoms: [AU1P]
abbr: Au
base: toppar_ions_won.str
charge: 1
name: Au<sup>+</sup>
AU3P:
atoms: [AU3P]
abbr: Au
base: toppar_ions_won.str
charge: 3
name: Au<sup>3+</sup>
CD2:
atoms: [CD]
abbr: Cd
base: toppar_water_ions.str
charge: 2
name: Cd<sup>2+</sup>
CO3P:
atoms: [CO3P]
abbr: Co
base: toppar_ions_won.str
charge: 3
name: Co<sup>3+</sup>
CR2P:
atoms: [CR2P]
abbr: Cr
base: toppar_ions_won.str
charge: 2
name: Cr<sup>2+</sup>
CR3P:
atoms: [CR3P]
abbr: Cr
base: toppar_ions_won.str
charge: 3
name: Cr<sup>3+</sup>
CU1P:
atoms: [CU1P]
abbr: Cu
base: toppar_ions_won.str
charge: 1
name: Cu<sup>+</sup>
CU2P:
atoms: [CU2P]
abbr: Cu
base: toppar_ions_won.str
charge: 2
name: Cu<sup>2+</sup>
FE2P:
atoms: [FE2P]
abbr: Fe
base: toppar_ions_won.str
charge: 2
name: Fe<sup>2+</sup>
FE3P:
atoms: [FE3P]
abbr: Fe
base: toppar_ions_won.str
charge: 3
name: Fe<sup>3+</sup>
HG2P:
atoms: [HG2P]
abbr: Hg
base: toppar_ions_won.str
charge: 2
name: Hg<sup>2+</sup>
MN2P:
atoms: [MN2P]
abbr: Mn
base: toppar_ions_won.str
charge: 2
name: Mn<sup>2+</sup>
MN3P:
atoms: [MN3P]
abbr: Mn
base: toppar_ions_won.str
charge: 3
name: Mn<sup>3+</sup>
NI2P:
atoms: [NI2P]
abbr: Ni
base: toppar_ions_won.str
charge: 2
name: Ni<sup>2+</sup>
PD2P:
atoms: [PD2P]
abbr: Pd
base: toppar_ions_won.str
charge: 2
name: Pd<sup>2+</sup>
PT2P:
atoms: [PT2P]
abbr: Pt
base: toppar_ions_won.str
charge: 2
name: Pt<sup>2+</sup>
RH3P:
atoms: [RH3P]
abbr: Rh
base: toppar_ions_won.str
charge: 3
name: Rh<sup>3+</sup>
SC3P:
atoms: [SC3P]
abbr: Sc
base: toppar_ions_won.str
charge: 3
name: Sc<sup>3+</sup>
TI1P:
atoms: [TI1P]
abbr: Ti
base: toppar_ions_won.str
charge: 1
name: Ti<sup>+</sup>
TI3P:
atoms: [TI3P]
abbr: Ti
base: toppar_ions_won.str
charge: 3
name: Ti<sup>3+</sup>
V2P:
atoms: [V2P]
abbr: V
base: toppar_ions_won.str
charge: 2
name: V<sup>2+</sup>
V3P:
atoms: [V3P]
abbr: V
base: toppar_ions_won.str
charge: 3
name: V<sup>3+</sup>
Y3P:
atoms: [Y3P]
abbr: Y
base: toppar_ions_won.str
charge: 3
name: Y<sup>3+</sup>
ZN2:
atoms: [ZN]
abbr: Zn
base: toppar_water_ions.str
charge: 2
name: Zn<sup>2+</sup>
post_transition_metals:
title: Post-Transition Metals
sub:
AL3P:
atoms: [AL3P]
abbr: Al
base: toppar_ions_won.str
charge: 3
name: Al<sup>3+</sup>
GA3P:
atoms: [GA3P]
abbr: Ga
base: toppar_ions_won.str
charge: 3
name: Ga<sup>3+</sup>
IN3P:
atoms: [IN3P]
abbr: In
base: toppar_ions_won.str
charge: 3
name: In<sup>3+</sup>
SN2P:
atoms: [SN2P]
abbr: Sn
base: toppar_ions_won.str
charge: 2
name: Sn<sup>2+</sup>
TL3P:
atoms: [TL3P]
abbr: Tl
base: toppar_ions_won.str
charge: 3
name: Tl<sup>3+</sup>
PB2P:
atoms: [PB2P]
abbr: Pb
base: toppar_ions_won.str
charge: 2
name: Pb<sup>2+</sup>
BI3P:
atoms: [BI3P]
abbr: Bi
base: toppar_ions_won.str
charge: 3
name: Bi<sup>3+</sup>
lanthanides:
title: Lanthanides
sub:
LA3P:
atoms: [LA3P]
abbr: La
base: toppar_ions_won.str
charge: 3
name: La<sup>3+</sup>
CE3P:
atoms: [CE3P]
abbr: Ce
base: toppar_ions_won.str
charge: 3
name: Ce<sup>3+</sup>
PR3P:
atoms: [PR3P]
abbr: Pr
base: toppar_ions_won.str
charge: 3
name: Pr<sup>3+</sup>
ND3P:
atoms: [ND3P]
abbr: Nd
base: toppar_ions_won.str
charge: 3
name: Nd<sup>3+</sup>
PM3P:
atoms: [PM3P]
abbr: Pm
base: toppar_ions_won.str
charge: 3
name: Pm<sup>3+</sup>
SM2P:
atoms: [SM2P]
abbr: Sm
base: toppar_ions_won.str
charge: 2
name: Sm<sup>2+</sup>
SM3P:
atoms: [SM3P]
abbr: Sm
base: toppar_ions_won.str
charge: 3
name: Sm<sup>3+</sup>
EU2P:
atoms: [EU2P]
abbr: Eu
base: toppar_ions_won.str
charge: 2
name: Eu<sup>2+</sup>
EU3P:
atoms: [EU3P]
abbr: Eu
base: toppar_ions_won.str
charge: 3
name: Eu<sup>3+</sup>
GD3P:
atoms: [GD3P]
abbr: Gd
base: toppar_ions_won.str
charge: 3
name: Gd<sup>3+</sup>
TB3P:
atoms: [TB3P]
abbr: Tb
base: toppar_ions_won.str
charge: 3
name: Tb<sup>3+</sup>
DY3P:
atoms: [DY3P]
abbr: Dy
base: toppar_ions_won.str
charge: 3
name: Dy<sup>3+</sup>
HO3P:
atoms: [HO3P]
abbr: Ho
base: toppar_ions_won.str
charge: 3
name: Ho<sup>3+</sup>
ER3P:
atoms: [ER3P]
abbr: Er
base: toppar_ions_won.str
charge: 3
name: Er<sup>3+</sup>
TU3P:
atoms: [TU3P]
abbr: Tm
base: toppar_ions_won.str
charge: 3
name: Tm<sup>3+</sup>
YB2P:
atoms: [YB2P]
abbr: Yb
base: toppar_ions_won.str
charge: 2
name: Yb<sup>2+</sup>
YB3P:
atoms: [YB3P]
abbr: Yb
base: toppar_ions_won.str
charge: 3
name: Yb<sup>3+</sup>
LU3P:
atoms: [LU3P]
abbr: Lu
base: toppar_ions_won.str
charge: 3
name: Lu<sup>3+</sup>
actinides:
title: Actinides
sub:
U3P:
atoms: [U3P]
abbr: U
base: toppar_ions_won.str
charge: 3
name: U<sup>3+</sup>
PU3P:
atoms: [PU3P]
abbr: Pu
base: toppar_ions_won.str
charge: 3
name: Pu<sup>3+</sup>
polyatomic_cations:
title: Polyatomic Cations
sub:
NH4:
abbr: NH<sub>4</sub>
base: top_all36_cgenff.rtf
charge: 1
name: Ammonium (NH<sub>4</sub><sup>+</sup>)
natoms: 5
anions:
title: Anion Type
sub:
polyatomic_anions:
title: Polyatomic Anions
sub:
ACET:
abbr: C<sub>2</sub>H<sub>3</sub>O<sub>2</sub>
base: top_all36_cgenff.rtf
charge: -1
name: Acetate (C<sub>2</sub>H<sub>3</sub>O<sub>2</sub><sup>-</sup>)
natoms: 7
ALF4:
abbr: AlF<sub>4</sub>
base: top_all36_cgenff.rtf
charge: -1
name: Aluminum Tetraflouride (AlF<sub>4</sub><sup>-</sup>)
natoms: 5
CO3:
abbr: CO<sub>3</sub>
base: top_all36_cgenff.rtf
charge: -2
name: Ionized Carbonate (CO<sub>3</sub><sup>2-</sup>)
natoms: 4
CO31:
abbr: CHO<sub>3</sub>
base: top_all36_cgenff.rtf
charge: -1
name: Bicarbonate (CHO<sub>3</sub><sup>-</sup>)
natoms: 5
FORA:
abbr: CHO<sub>2</sub>
base: top_all36_cgenff.rtf
charge: -1
name: Formate (CHO<sub>2</sub><sup>-</sup>)
natoms: 4
MES1:
abbr: CH<sub>3</sub>S
base: top_all36_cgenff.rtf
charge: -1
name: Methylthiolate (CH<sub>3</sub>S<sup>-</sup>)
natoms: 5
METO:
abbr: CH<sub>3</sub>O
base: top_all36_cgenff.rtf
charge: -1
name: Methoxide (CH<sub>3</sub>O<sup>-</sup>)
natoms: 5
OH:
abbr: OH
base: toppar_water_ions.str
charge: -1
name: Hydroxide Ion (OH<sup>-</sup>)
natoms: 2
PO4:
abbr: PO<sub>4</sub>
base: toppar_all36_moreions.str
name: Phosphate (PO<sub>4</sub><sup>3-</sup>)
charge: -3
natoms: 5
HPO4:
abbr: HPO<sub>4</sub>
base: toppar_all36_moreions.str
name: Hydrogen Phosphate (HPO<sub>4</sub><sup>2-</sup>)
charge: -2
natoms: 6
H2PO4:
abbr: H<sub>2</sub>PO<sub>4</sub>
base: toppar_all36_moreions.str
name: Dihydrogen phosphate (H<sub>2</sub>PO<sub>4</sub><sup>-</sup>)
charge: -1
natoms: 7
SO4:
abbr: SO<sub>4</sub>
base: toppar_all36_moreions.str
name: Sulfate (SO<sub>4</sub><sup>2-</sup>)
charge: -2
natoms: 5
HSO4:
abbr: HPO<sub>4</sub>
base: toppar_all36_moreions.str
name: Hydrogen Sulfate (HPO<sub>4</sub><sup>-</sup>)
charge: -1
natoms: 6
halogens:
title: Halogens
sub:
CLA:
abbr: Cl
atoms: [CLA]
base: toppar_water_ions.str
charge: -1
name: Cl<sup>-</sup>