Universal molecule and atom names
Molecule names
To enable automatic analyses over all simulations, universal names for molecules are defined in the NMRlipids databank 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 NMRlipids databank 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 from the NMRlipids databank git.
If you are adding data into the databank and a mapping file for your molecule(s) do not exist, you need to create a new one and add it to the NMRlipids databank git. Easiest is to take similar already existing mapping file and modify that. If atoms in a lipid belong to different residues (typical situation in Amber force fields, for example see here), add the residue name to RESIDUE key of each atom in the mapping file. In this case, give the name of the head group residue in the COMPOSITION dictionary in the README.yaml file. If your simulation contains molecules that are not yet in the databank, you need to define the abbreviation and add molecules to the lipids_dict or molecules_dict in the databankLibrary.py, as well as to the table above. Please do not hesitate to ask assistance via GitHub issues. The mapping file should contain all the atoms of the molecules.