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:

CA

N

O

C

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.

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

Nucleic backbone

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

C5’

O3’

C3’

P

O5’

Nucleobases

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

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

Nucleic sugars

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

C2’

C4’

C1’

C3’

O4’