Universal molecule and atom names

Molecule names

To enable automatic analyses over all simulations, universal names for molecules are defined in the FAIRMD Lipids as listed in the table below. These names are connected to simulation specific molecule names using the COMPOSITION dictionary in README.yaml files.

Abbreviation

Molecule name

POPC

1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

POPG

1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol

POPS

1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine

POPE

1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine

PYPC

1-(16:0)-2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine

PAzePCprot

1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine protonated

PAzePCdeprot

1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine deprotonated

DMPC

1,2-dimyristoyl-sn-glycero-3-phosphocholine

DPPC

1,2-dipalmitoyl-sn-glycero-3-phosphocholine

DPPE

1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine

DPPG

1,2-dipalmitoyl-sn-glycero-3-phospho-(1’-rac-glycerol) (sodium salt)

DEPC

1,2-dierucoyl-sn-glycero-3-phosphocholine

DRPC

1,2-(14:1$^\Delta9$)-sn-glycero-3-phosphocholine

DYPC

1,2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine

DLPC

1,2-dilauroyl-sn-glycero-3-phosphocholine

DLIPC

1,2-dilinoleoyl-sn-glycero-3-phosphocholine

DOG

1,2-dioleoyl-sn-glycerol

DOPC

1,2-dioleoyl-sn-glycero-3-phosphocholine

DOPE

1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

DDOPC

1,2-didocosahexaenoyl-sn-glycero-3-phosphocholine

DOPS

1,2-dioleoyl-sn-glycero-3-phospho-L-serine

DSPC

1,2-distearoyl-sn-glycero-3-phosphocholine

DAPC

1,2-diarachidonoyl-sn-glycero-3-phosphocholine

SLiPC

1-(18:0)-2-(18:2 $^{\Delta9,12}$)-sn-glycero-3-phosphocholine

DMTAP

1,2-dimyristoyl-3-trimethylammonium-propane

GM1

GM1 Ganglioside

SOPC

1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine

POPI

1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol

SAPI

1-stearoyl-2-arachidonoyl-sn-glycero-3-phosphoinositol

SAPI24

1-stearoyl-2-arachidonoyl-sn-glycero-3-phospho-(1’-myo-inositol-4’,5’-bisphosphate)

SLPI

1-stearoyl-2-lauroyl-sn-glycero-3-phosphoinositol

SDG

1-stearoyl-2-docosahexaenoyl-sn-glycerol

SDPE

1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphoethanolamine

SM16

N-palmitoyl-D-erythro-sphingosylphosphorylcholine

SM18

N-stearoyl-D-erythro-sphingosylphosphorylcholine

TOCL

1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol

TLCL

tetralinoleoyl cardiolipin

CER

N-palmitoyl-D-erythro-sphingosine

CER180

N-stearoyl-D-erythro-sphingosine

CHOL

cholesterol

DCHOL

18,19-di-nor-cholesterol

DHMDMAB

dihexadecyldimethylammonium

DPPGK

1,2-dioleoyl-sn-glycero-3-[phospho-rac-(3-lysyl(1-glycerol))] (lysyl-PG)

POT

potassium ion

SOD

sodium ion

CLA

chloride ion

CAL

calcium ion

CES

caesium ion

C20

n-eicosane

SOL

water

Universal atom names in mapping files

To enable automatic analyses over all simulations, universal atom names for each molecule are defined in the FAIRMD Lipids using the mapping files. In these files, universal atom names are connected to simulation specific atom names using python dictionaries stored in yaml file format. The first key in the mapping file dictionary is the universal atom name, second keys define the simulation specific atom name (ATOMNAME) and molecule fragment (FRAGMENT: head group, glycerol backbone, sn-1 or sn-2). For example, the beginning of the mapping file for CHARMM36 POPC looks like this:

 M_G1_M:
  ATOMNAME: C3
  FRAGMENT: glycerol backbone
M_G1H1_M:
  ATOMNAME: HX
  FRAGMENT: glycerol backbone
M_G1H2_M:
  ATOMNAME: HY
  FRAGMENT: glycerol backbone
M_G1O1_M:
  ATOMNAME: O31
  FRAGMENT: glycerol backbone
M_G1C2_M:
  ATOMNAME: C31
  FRAGMENT: sn-1
M_G1C2O1_M:
  ATOMNAME: O32
  FRAGMENT: sn-1
.
.
.

Universal atom names start with “M_” flag and ends with “_M” flag. In the actual naming convention between the flags, the first two characters define in which glycerol backbone chain the atoms attached (G1, G2 or G3), third character tells the atom type and fourth character tells the counting number from the glycerol backbone carbon. If there are hydrogens or other atoms attached to the main chain, those will be added to the end of the naming. More details can be found from the original NMRlipids project post defining the mapping files. Examples already existing mapping files can be found in the Toy Databank.

Cardiolipin universal naming conventions

If you add a lipid of this family, you can stick to following namings:

                        G02O1
                    G01--G02--G03
                  /               \
               G23P1O1           G13P1O1
  G23P1O[2/3]--G23P1             G13P1--G12P1O[2/3]
               G23O1             G13O1
                 |                |
   G22C2O1       G23              G13         G12C2O1
   ||            |                |            ||
   G22C2--G22O1--G22              G12--G12O1--G12C2
  G22C3          |                |            G12C3
 G22C4           G21              G11           G12C4
 ..           G21O1                G11O1          ..
      G21C2O1==G21C2              G11C2==G11C2O1
                G21C3              G11C3
               G32C4              G11C4
                ..                 ..