Standard residues in MDAnalysis selections
Proteins
The residue names listed here are accessible via the “protein” keyword in the Atom selection language.
The below names are drawn from the CHARMM 27, OPLS-AA, GROMOS 53A6, AMBER 03, and AMBER 99sb*-ILDN force fields.
ACE |
ALA |
ALAD |
ARG |
ARGN |
ASF |
ASH |
ASN |
ASN1 |
ASP |
ASPH |
CALA |
CARG |
CASF |
CASN |
CASP |
CCYS |
CCYX |
CGLN |
CGLU |
CGLY |
CHID |
CHIE |
CHIP |
CILE |
CLEU |
CLYS |
CME |
CMET |
CPHE |
CPRO |
CSER |
CTHR |
CTRP |
CTYR |
CVAL |
CYM |
CYS |
CYS1 |
CYS2 |
CYSH |
CYX |
DAB |
GLH |
GLN |
GLU |
GLUH |
GLY |
HID |
HIE |
HIP |
HIS |
HIS1 |
HIS2 |
HISA |
HISB |
HISD |
HISE |
HISH |
HSD |
HSE |
HSP |
HYP |
ILE |
LEU |
LYN |
LYS |
LYSH |
MET |
MSE |
NALA |
NARG |
NASN |
NASP |
NCYS |
NCYX |
NGLN |
NGLU |
NGLY |
NHID |
NHIE |
NHIP |
NILE |
NLEU |
NLYS |
NME |
NMET |
NPHE |
NPRO |
NSER |
NTHR |
NTRP |
NTYR |
NVAL |
ORN |
PGLU |
PHE |
PRO |
QLN |
SER |
THR |
TRP |
TYR |
VAL |
Protein backbone
Protein backbone atoms in MDAnalysis belong to a recognised protein residue and have the atom names:
O |
CA |
C |
N |
Nucleic acids
The residue names listed here are accessible via the “nucleic” keyword in the Atom selection language.
The below names are drawn from largely from the CHARMM force field.
RA |
C |
RA5 |
DG5 |
RG |
THY |
DT |
ADE |
DC |
RU5 |
RC5 |
RG3 |
G |
DC5 |
RU |
DA5 |
RC3 |
DG |
DG3 |
DT3 |
RU3 |
RC |
URA |
DC3 |
DA3 |
T |
A |
CYT |
DT5 |
RG5 |
U |
DA |
GUA |
RA3 |
Nucleic backbone
Nucleic backbone atoms in MDAnalysis belong to a recognised nucleic acid residue and have the atom names:
C5’ |
C3’ |
O5’ |
O3’ |
P |
Nucleobases
Nucleobase atoms from nucleic acid residues are recognised based on their names in CHARMM.
O4 |
N4 |
N1 |
N3 |
N9 |
N7 |
O6 |
C4 |
O2 |
C2 |
N2 |
C6 |
C5 |
N6 |
C8 |
C5M |
Nucleic sugars
Nucleic sugar atoms from nucleic acid residues are recognised by MDAnalysis if they have the atom names:
C1’ |
C2’ |
O4’ |
C3’ |
C4’ |