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

O

CA

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.

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

Nucleic backbone

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

C5’

P

O5’

C3’

O3’

Nucleobases

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

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

Nucleic sugars

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

C2’

C1’

C3’

C4’

O4’