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:

C

N

O

CA

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.

RA3	URA	RC3	A	ADE	THY	RA	DG5
T	RG	DG3	DT	C	DA3	U	RG3
RA5	RU	RU3	GUA	DT5	G	DA5	CYT
RU5	RC	DG	RG5	DC	DT3	DC5	DC3
RC5	DA

Nucleic backbone

Nucleic backbone atoms in MDAnalysis belong to a recognised nucleic acid residue and have the atom names:

O3’

C5’

C3’

P

O5’

Nucleobases

Nucleobase atoms from nucleic acid residues are recognised based on their names in CHARMM.

N1	N4	N9	N6	C5	N3	O6	C8
N7	N2	C2	C5M	C6	C4	O2	O4

Nucleic sugars

Nucleic sugar atoms from nucleic acid residues are recognised by MDAnalysis if they have the atom names:

C3’

C1’

C2’

O4’

C4’