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:

N

CA

C

O

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

DC5

DT3

DG

DG5

DT

RG5

DA3

THY

RA

RU5

DC3

A

T

RA3

G

RG3

URA

DT5

RC5

RA5

RU3

DA

DG3

RC

GUA

DC

RC3

RG

RU

C

CYT

U

ADE

Nucleic backbone

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

O3’

P

C5’

C3’

O5’

Nucleobases

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

N1

N6

O6

N3

C2

C5

O4

C8

N4

N2

O2

C5M

N9

N7

C6

C4

Nucleic sugars

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

C2’

C1’

C3’

C4’

O4’