attribute: amberName
none handling: delete
recipient: residues

# start out by assigning most residues their own names as a default

# ... standard amino acids

	:ALA	ALA

	:ARG	ARG

	:ASN	ASN

	:ASP	ASP

	:CYS	CYS

	:GLN	GLN

	:GLU	GLU

	:GLY	GLY

	:HID	HID
	:HIE	HIE
	:HIP	HIP

	:ILE	ILE

	:LEU	LEU

	:LYS	LYS

	:MET	MET

	:PHE	PHE

	:PRO	PRO

	:SER	SER

	:THR	THR

	:TRP	TRP

	:TYR	TYR

	:VAL	VAL

# ... modified/non-standard amino acids

	:NME	NME

	:NHE	NHE

	:ACE	ACE

# ... nucleic acids, defaulting to DNA name, since it is easier to

# select RNA later to override the name

	:A	DA
	:RA	RA
	:RA3	RA3
	:RA5	RA5
	:DA3	DA3
	:DA5	DA5

	:C	DC
	:RC	RC
	:RC3	RC3
	:RC5	RC5
	:DC3	DC3
	:DC5	DC5

	:G	DG
	:RG	RG
	:RG3	RG3
	:RG5	RG5
	:DG3	DG3
	:DG5	DG5

	:T	DT
	:DT	DT
	:DT3	DT3
	:DT5	DT5

	:U	RU
	:RU	RU
	:RU3	RU3
	:RU5	RU5

	:DA	DA

	:DC	DC

	:DG	DG

	:DT	DT

# ... misc

	:.water	HOH
# some PDBs have waters with actual chain IDs; catch those
	:HOH	HOH
	:DOD	HOH

# highly negatively charged residues cause sqm failures
# use templates for commonplace ones
	:ADP	ADP
	:ADP@H1B	None
	:ADP@H2B	None
	:ADP@H3B	None
	:ATP	ATP
	:ATP@H1G	None
	:ATP@H2G	None
	:ATP@H3G	None
	:GDP	GDP
	:GDP@H1B	None
	:GDP@H2B	None
	:GDP@H3B	None
	:GTP	GTP
	:GTP@H1G	None
	:GTP@H2G	None
	:GTP@H3G	None

# find RNA and override name

	:A@o2'	RA

	:C@o2'	RC

	:G@o2'	RG

# histidine protonation states

	:HI?@hd1	HID
	:HI?@dd1	HID
	:HI?@td1	HID

	:HI?@he2	HIE
	:HI?@de2	HIE
	:HI?@te2	HIE

	:/amberName="HIE"@hd1	HIP
	:/amberName="HIE"@dd1	HIP
	:/amberName="HIE"@td1	HIP

# di-sulfide CYS

	:CY? & disulfide	CYX

# negative CYS

	:/amberName="CYS"	CYM

	:CYS@hg	CYS

# protonated aspartic/glutamic acid

	:AS?@od? & @/idatmType=O3	ASH

	:GL?@oe? & @/idatmType=O3	GLH

# neutral lysine

	:LY?@nz  & @/idatmType=N3	LYN

# chain-terminal variants

	:/amberName=ALA @oxt	CALA

	:/amberName=ARG @oxt	CARG

	:/amberName=ASH @oxt	CASH

	:/amberName=ASN @oxt	CASN

	:/amberName=ASP @oxt	CASP

	:/amberName=CYM @oxt	CCYM

	:/amberName=CYS @oxt	CCYS

	:/amberName=CYX @oxt	CCYX

	:/amberName=GLH @oxt	CGLH

	:/amberName=GLN @oxt	CGLN

	:/amberName=GLU @oxt	CGLU

	:/amberName=GLY @oxt	CGLY

	:/amberName=HID @oxt	CHID

	:/amberName=HIE @oxt	CHIE

	:/amberName=HIP @oxt	CHIP

	:/amberName=ILE @oxt	CILE

	:/amberName=LEU @oxt	CLEU

	:/amberName=LYN @oxt	CLYN

	:/amberName=LYS @oxt	CLYS

	:/amberName=MET @oxt	CMET

	:/amberName=PHE @oxt	CPHE

	:/amberName=PRO @oxt	CPRO

	:/amberName=SER @oxt	CSER

	:/amberName=THR @oxt	CTHR

	:/amberName=TRP @oxt	CTRP

	:/amberName=TYR @oxt	CTYR

	:/amberName=VAL @oxt	CVAL

	:/amberName=ALA @N & @/idatmType=N3+	NALA

	:/amberName=ARG @N & @/idatmType=N3+	NARG

	:/amberName=ASH @N & @/idatmType=N3+	NASH

	:/amberName=ASN @N & @/idatmType=N3+	NASN

	:/amberName=ASP @N & @/idatmType=N3+	NASP

	:/amberName=CYM @N & @/idatmType=N3+	NCYM

	:/amberName=CYS @N & @/idatmType=N3+	NCYS

	:/amberName=CYX @N & @/idatmType=N3+	NCYX

	:/amberName=GLH @N & @/idatmType=N3+	NGLH

	:/amberName=GLN @N & @/idatmType=N3+	NGLN

	:/amberName=GLU @N & @/idatmType=N3+	NGLU

	:/amberName=GLY @N & @/idatmType=N3+	NGLY

	:/amberName=HID @N & @/idatmType=N3+	NHID

	:/amberName=HIE @N & @/idatmType=N3+	NHIE

	:/amberName=HIP @N & @/idatmType=N3+	NHIP

	:/amberName=ILE @N & @/idatmType=N3+	NILE

	:/amberName=LEU @N & @/idatmType=N3+	NLEU

	:/amberName=LYN @N & @/idatmType=N3+	NLYN

	:/amberName=LYS @N & @/idatmType=N3+	NLYS

	:/amberName=MET @N & @/idatmType=N3+	NMET

	:/amberName=PHE @N & @/idatmType=N3+	NPHE

	:/amberName=PRO @N & @/idatmType=N3+	NPRO

	:/amberName=SER @N & @/idatmType=N3+	NSER

	:/amberName=THR @N & @/idatmType=N3+	NTHR

	:/amberName=TRP @N & @/idatmType=N3+	NTRP

	:/amberName=TYR @N & @/idatmType=N3+	NTYR

	:/amberName=VAL @N & @/idatmType=N3+	NVAL

	:/amberName="DA"@h3t	DA3

	:/amberName="DC"@h3t	DC3

	:/amberName="DG"@h3t	DG3

	:/amberName="DT"@h3t	DT3

	:/amberName="RA"@h3t	RA3

	:/amberName="RC"@h3t	RC3

	:/amberName="RG"@h3t	RG3

	:/amberName="RU"@h3t	RU3

	:/amberName="DA"@h5t	DA5

	:/amberName="DC"@h5t	DC5

	:/amberName="DG"@h5t	DG5

	:/amberName="DT"@h5t	DT5

	:/amberName="RA"@h5t	RA5

	:/amberName="RC"@h5t	RC5

	:/amberName="RG"@h5t	RG5

	:/amberName="RU"@h5t	RU5

	:/amberName="DA5"@h3t	DAN

	:/amberName="DC5"@h3t	DCN

	:/amberName="DG5"@h3t	DGN

	:/amberName="DT5"@h3t	DTN

	:/amberName="RA5"@h3t	RAN

	:/amberName="RC5"@h3t	RCN

	:/amberName="RG5"@h3t	RGN

	:/amberName="RU5"@h3t	RUN

	:/amberName="DA"@ho3'	DA3

	:/amberName="DC"@ho3'	DC3

	:/amberName="DG"@ho3'	DG3

	:/amberName="DT"@ho3'	DT3

	:/amberName="RA"@ho3'	RA3

	:/amberName="RC"@ho3'	RC3

	:/amberName="RG"@ho3'	RG3

	:/amberName="RU"@ho3'	RU3

	:/amberName="DA"@ho5'	DA5

	:/amberName="DC"@ho5'	DC5

	:/amberName="DG"@ho5'	DG5

	:/amberName="DT"@ho5'	DT5

	:/amberName="RA"@ho5'	RA5

	:/amberName="RC"@ho5'	RC5

	:/amberName="RG"@ho5'	RG5

	:/amberName="RU"@ho5'	RU5

	:/amberName="DA5"@ho3'	DAN

	:/amberName="DC5"@ho3'	DCN

	:/amberName="DG5"@ho3'	DGN

	:/amberName="DT5"@ho3'	DTN

	:/amberName="RA5"@ho3'	RAN

	:/amberName="RC5"@ho3'	RCN

	:/amberName="RG5"@ho3'	RGN

	:/amberName="RU5"@ho3'	RUN