Cerius2 Forcefield Based Simulations - Forcefield Terms and Atom Types

Forcefield Based Simulations

B Forcefield Terms and Atom Types

This appendix explains

This appendix includes tables of atom types for these forcefields:

: Original AMBER here
: Homans' AMBER here
: CFF91 here
: CHARMm here
: COMPASS here
: CVFF here
: CVFF_aug here
: ESFF here
: PCFF here

This appendix also includes a table of definitions of individual terms found in various forcefields (Forcefield term definitions).

Examining forcefield files

You can examine the forcefield files directly for atom types and other information (for information on how to edit these files, please see Editing a forcefield):

For the Insight molecular modeling program, human-readable forcefield files are found in $BIOSYM_LIBRARY/*.frc
For Cerius²·OFF, human-readable forcefield files are found in the C²_installation_directory/Cerius2-Resources/FORCE-FIELD directory (the Cerius2-Resources/FORCE-FIELD directory also appears in the directory in which you run Cerius²).
For CHARMm, the human-readable forcefield parameter files are located in $CHM_DATA/*PRM. The atom types are in the $CHM_DATA/MASSES.RTF file.

Forcefield term definitions

Table 24 . Common potential terms in major forcefields supported by MSI

name illustrated form of the term forcefield¹
quadratic bond-stretching

AMBER, CHARMm, UFF

quartic bond-stretching

CFF

Morse bond-stretching

CVFF, ESFF

quadratic angle-bending

AMBER, CHARMm, CVFF

quartic angle-bending

CFF

cosine angle-bending
various
ESFF, UFF

single-cosine torsion

or similar
AMBER, CHARMm,
CVFF

three-term cosine torsion

CFF

cosine-Fourier torsion

UFF

sin-cos torsion

ESFF

improper cosine out-of-plane

or similar
AMBER, CVFF, UFF

improper quadratic out-of-plane

CHARMm

improper square out-of-plane, imprope

CVFF

Wilson (or umbrella) out-of-plane

CFF, ESFF, UFF

UFF

pyrimid-height out-of-plane

not used
none

6-9 van der Waals

or
CFF, ESFF, UFF

6-12 van der Waals
or
AMBER, CHARMm, CVFF

electrostatic
or similar
AMBER, CFF, CHARMm,CVFF, ESFF, UFF

quadratic bond-bond

CFF, CVFF ²

quadratic bond-angle

CFF, CVFF

angle-angle

CFF, CVFF

end bond-torsion

CFF

center bond-torsion

CFF

angle-torsion

CFF

angle-angle-torsion

CFF, CVFF

improper out-of-plane--out-of-plane, improper

CVFF

¹ Major forcefields, for the purposes of this table, are AMBER, CFF, CHARMm, CVFF, ESFF, UFF.
² AMBER, CHARMm, ESFF, and UFF contain no cross terms.

Table 24 . Common potential terms in major forcefields supported by MSI
name	illustrated	form of the term	forcefield¹
quadratic bond-stretching			AMBER, CHARMm, UFF
quartic bond-stretching		CFF
Morse bond-stretching		CVFF, ESFF
quadratic angle-bending			AMBER, CHARMm, CVFF
quartic angle-bending		CFF
cosine angle-bending	various	ESFF, UFF
single-cosine torsion		or similar	AMBER, CHARMm, CVFF
three-term cosine torsion		CFF
cosine-Fourier torsion		UFF
sin-cos torsion		ESFF
improper cosine out-of-plane		or similar	AMBER, CVFF, UFF
improper quadratic out-of-plane		CHARMm
improper square out-of-plane, imprope		CVFF
Wilson (or umbrella) out-of-plane			CFF, ESFF, UFF
	UFF
pyrimid-height out-of-plane		not used	none
6-9 van der Waals		or	CFF, ESFF, UFF
6-12 van der Waals	or	AMBER, CHARMm, CVFF
electrostatic	or similar	AMBER, CFF, CHARMm,CVFF, ESFF, UFF
quadratic bond-bond			CFF, CVFF ²
quadratic bond-angle			CFF, CVFF
angle-angle			CFF, CVFF
end bond-torsion			CFF
center bond-torsion			CFF
angle-torsion			CFF
angle-angle-torsion			CFF, CVFF
improper out-of-plane--out-of-plane, improper			CVFF

AMBER atom types

Standard AMBER forcefield

Table 25 . Atom types--AMBER (Page 1 of 4)

general class atom type¹ description
hydrogen types

H
amide or imino hydrogen

HC
explicit hydrogen attached to carbon

HO
hydrogen on hydroxyl oxygen

HS
hydrogen attached to sulfur

HW
hydrogen in water

H2
amino hydrogen in NH₂

H3
hydrogen of lysine or arginine (positively charged)

all-atom carbon types²

C
sp² carbonyl carbon and aromatic carbon with hydroxyl substituent in tyrosine

CA
sp² aromatic carbon in 6-membered ring with 1 substituent

CB
sp² aromatic carbon at junction between 5- and 6-membered rings

CC
sp² aromatic carbon in 5-membered ring with 1 substituent and next to a nitrogen

CK
sp² aromatic carbon in 5-membered ring between 2 nitrogens and bonded to 1 hydrogen (in purine)

CM
sp² same as CJ but one substituent

CN
sp² aromatic junction carbon in between 5- and 6-membered rings

CQ
sp² carbon in 6-membered ring of purine between 2 NC nitrogens and bonded to 1 hydrogen

CR
sp² aromatic carbon in 5-membered ring between 2 nitrogens and bonded to 1 H (in his)

CT
sp³ carbon with 4 explicit substituents

CV
sp² aromatic carbon in 5-membered ring bonded to 1 N and bonded to an explicit hydrogen

CW
sp² aromatic carbon in 5-membered ring bonded to 1 N-H and bonded to an explicit hydrogen

C*
sp² aromatic carbon in 5-membered ring with 1 substituent

united carbon types³

CD
sp² aromatic carbon in 6-membered ring with 1 hydrogen

CE
sp² aromatic carbon in 5-membered ring between 2 nitrogens with 1 hydrogen (in purines)

CF
sp² aromatic carbon in 5-membered ring next to a nitrogen without a hydrogen

CG
sp² aromatic carbon in 5-membered ring next to an N-H

CH
sp³ carbon with 1 hydrogen

CI
sp² carbon in 6-membered ring of purines between 2 NC nitrogens

CJ
sp² carbon in pyrimidine at positions 5 or 6 (more pure double bond than aromatic with 1 hydrogen)

CP
sp² aromatic carbon in 5-membered ring between 2 nitrogens with one hydrogen (in his)

C2
sp³ carbon with 2 hydrogens

C3
sp³ carbon with 3 hydrogens

nitrogen types

N
sp² nitrogen in amide group

NA
sp² nitrogen in 5-membered ring with hydrogen attached

NB
sp² nitrogen in 5-membered ring with lone pairs

NC
sp² nitrogen in 6-membered ring with lone pairs

NT
sp³ nitrogen with 3 substituents

N2
sp² nitrogen in base NH₂ group or arginine NH₂

N3
sp³ nitrogen with 4 substituents

N*
sp² nitrogen in purine or pyrimidine with alkyl group attached

oxygen types

O
carbonyl oxygen

OH
alcohol oxygen

OS
ether or ester oxygen

OW
water oxygen

O2
carboxyl or phosphate nonbonded oxygen

sulfur types

S
sulfur in disulfide linkage or methionine

SH
sulfur in cystine

phosphorus

P
phosphorus in phosphate group

ion types

CU
copper ion (Cu⁺²)

CØ
calcium ion (Ca⁺²)

I
iodine ion (I^-)

IM
chlorine ion (Cl^-)

MG
magnesium ion (Mg⁺²)

QC
cesium ion (Cs⁺)

QK
potassium ion (K⁺)

QL
lithium ion (Li⁺)

QN
sodium ion (Na⁺)

QR
rubidium ion (Rb⁺)

other

LP
lone pair

¹ From Weiner et al. (1984) and Weiner et al. (1986).
² Non-hydrogen-containing carbons.
³ United-atom carbons with implicit inclusion of hydrogens.

Table 25 . Atom types--AMBER (Page 1 of 4)
general class	atom type¹	description
hydrogen types
	H	amide or imino hydrogen
	HC	explicit hydrogen attached to carbon
	HO	hydrogen on hydroxyl oxygen
	HS	hydrogen attached to sulfur
	HW	hydrogen in water
	H2	amino hydrogen in NH₂
	H3	hydrogen of lysine or arginine (positively charged)
all-atom carbon types²
	C	sp² carbonyl carbon and aromatic carbon with hydroxyl substituent in tyrosine
	CA	sp² aromatic carbon in 6-membered ring with 1 substituent
	CB	sp² aromatic carbon at junction between 5- and 6-membered rings
	CC	sp² aromatic carbon in 5-membered ring with 1 substituent and next to a nitrogen
	CK	sp² aromatic carbon in 5-membered ring between 2 nitrogens and bonded to 1 hydrogen (in purine)
	CM	sp² same as CJ but one substituent
	CN	sp² aromatic junction carbon in between 5- and 6-membered rings
	CQ	sp² carbon in 6-membered ring of purine between 2 NC nitrogens and bonded to 1 hydrogen
	CR	sp² aromatic carbon in 5-membered ring between 2 nitrogens and bonded to 1 H (in his)
	CT	sp³ carbon with 4 explicit substituents
	CV	sp² aromatic carbon in 5-membered ring bonded to 1 N and bonded to an explicit hydrogen
	CW	sp² aromatic carbon in 5-membered ring bonded to 1 N-H and bonded to an explicit hydrogen
	C*	sp² aromatic carbon in 5-membered ring with 1 substituent
united carbon types³
	CD	sp² aromatic carbon in 6-membered ring with 1 hydrogen
	CE	sp² aromatic carbon in 5-membered ring between 2 nitrogens with 1 hydrogen (in purines)
	CF	sp² aromatic carbon in 5-membered ring next to a nitrogen without a hydrogen
	CG	sp² aromatic carbon in 5-membered ring next to an N-H
	CH	sp³ carbon with 1 hydrogen
	CI	sp² carbon in 6-membered ring of purines between 2 NC nitrogens
	CJ	sp² carbon in pyrimidine at positions 5 or 6 (more pure double bond than aromatic with 1 hydrogen)
	CP	sp² aromatic carbon in 5-membered ring between 2 nitrogens with one hydrogen (in his)
	C2	sp³ carbon with 2 hydrogens
	C3	sp³ carbon with 3 hydrogens
nitrogen types
	N	sp² nitrogen in amide group
	NA	sp² nitrogen in 5-membered ring with hydrogen attached
	NB	sp² nitrogen in 5-membered ring with lone pairs
	NC	sp² nitrogen in 6-membered ring with lone pairs
	NT	sp³ nitrogen with 3 substituents
	N2	sp² nitrogen in base NH₂ group or arginine NH₂
	N3	sp³ nitrogen with 4 substituents
	N*	sp² nitrogen in purine or pyrimidine with alkyl group attached
oxygen types
	O	carbonyl oxygen
	OH	alcohol oxygen
	OS	ether or ester oxygen
	OW	water oxygen
	O2	carboxyl or phosphate nonbonded oxygen
sulfur types
	S	sulfur in disulfide linkage or methionine
	SH	sulfur in cystine
phosphorus
	P	phosphorus in phosphate group
ion types
	CU	copper ion (Cu⁺²)
	CØ	calcium ion (Ca⁺²)
	I	iodine ion (I^-)
	IM	chlorine ion (Cl^-)
	MG	magnesium ion (Mg⁺²)
	QC	cesium ion (Cs⁺)
	QK	potassium ion (K⁺)
	QL	lithium ion (Li⁺)
	QN	sodium ion (Na⁺)
	QR	rubidium ion (Rb⁺)
other
	LP	lone pair

Homan's carbohydrate forcefield

Table 26 . Atom types--Homans

general class atom type description
carbohydrate-hydrogen types

AH
anomeric hydrogen

BH
anomeric hydrogen

HT
sp³ hydrogen

HY
hydroxyl hydrogen

carbohydrate-carbon types

AC
anomeric carbon

BC
anomeric carbon

CS
sp³ carbon in sugar ring

carbohydrate-oxygen types

OA
anomeric oxygen

OB
anomeric oxygen

OE
ring oxygen

OT
hydroxyl oxygen

Table 26 . Atom types--Homans
general class	atom type	description
carbohydrate-hydrogen types
	AH	anomeric hydrogen
	BH	anomeric hydrogen
	HT	sp³ hydrogen
	HY	hydroxyl hydrogen
carbohydrate-carbon types
	AC	anomeric carbon
	BC	anomeric carbon
	CS	sp³ carbon in sugar ring
carbohydrate-oxygen types
	OA	anomeric oxygen
	OB	anomeric oxygen
	OE	ring oxygen
	OT	hydroxyl oxygen

CFF91 atom types

Table 27 . Atom types--CFF91 (Page 1 of 4)

general class atom type description
hydrogen types

dw
deuterium in heavy water (equiv. to h)

h
hydrogen bonded to C or S

hc
hydrogen bonded to C (equiv. to h)

hi
hydrogen in charged imidazole ring

hn
hydrogen bonded to N (equiv. to h)

ho
hydrogen bonded to O (equiv. to h)

hp
hydrogen bonded to P (equiv. to h)

hs
hydrogen bonded to S (equiv. to h)

hw
hydrogen in water (equiv. to h)

h*
polar hydrogen bonded to N or O

h+
charged hydrogen (in cation)

carbon types

c
generic sp³ carbon

ca
general amino acid alpha carbon (sp³) (equiv. to c)

cg
sp³ alpha carbon in glycine (equiv. to c)

ci
sp² aromatic carbon in charged imidazole ring (his⁺) (equiv. to cp)

co
sp³ carbon in acetal (equiv. to c)

coh
sp³ carbon in acetal with hydrogen (equiv. to c)

cp
sp² aromatic carbon

cr
carbon in guanidinium group (HN=C(NH₂)₂) (arg)

cs
sp² carbon in 5-membered ring next to S (equiv. to cp)

ct
sp carbon involved in triple bond

c1
sp³ carbon bonded to 1 H, 3 heavy atoms (equiv. to c)

c2
sp³ carbon bonded to 2 H's, 2 heavy atoms (equiv. to c)

c3
sp³ carbon in methyl (CH₃) group (equiv. to c)

c5
sp² aromatic carbon in 5-membered ring (equiv. to cp)

c3h
sp³ carbon in 3-membered ring with hydrogens (equiv. to c)

c3m
sp³ carbon in 3-membered ring (equiv. to c)

c4h
sp³ carbon in 4-membered ring with hydrogens (equiv. to c)

c4m
sp³ carbon in 4-membered ring (equiv. to c)

c´
sp² carbon in carbonyl (C=O) group in amide

c"
carbon in carbonyl group, not amide (equiv. to c)

c
carbon in carbonyl group, not amide

c-
carbon in carboxylate (COO^-) group

c+
carbon in guanidinium group

c=
nonaromatic end doubly bonded carbon

c=1
nonaromatic, next-to-end doubly bonded carbon

c=2
nonaromatic doubly bonded carbon

nitrogen types

n
sp² amide nitrogen

na
sp³ amine nitrogen

nb
sp² nitrogen in aromatic amine (equiv. to nn)

nh
sp² nitrogen in 5- or 6-membered ring, bonded to hydrogen

nho
sp² nitrogen in 6-membered ring, next to a carbonyl group and with a hydrogen (equiv. to nh)

nh+
protonated nitrogen in 6-membered ring

ni
sp² nitrogen in charged imidazole ring (his⁺) (equiv. to nh)

nn
sp² nitrogen in aromatic amine

np
sp² nitrogen in 5- or 6-membered ring, not bonded to hydrogen

npc
sp² nitrogen in 5- or 6-membered ring, bonded to a heavy atom (equiv. to nh)

nr
sp² nitrogen in guanidinium group (HN=C(NH₂)₂)

nt
sp nitrogen involved in triple bond

nz
sp nitrogen in N₂

n1
sp² nitrogen in charged arginine (equiv. to nr)

n2
sp² nitrogen in guanidinium group (HN=C(NH₂)₂) (equiv. to nr)

n4
sp³ nitrogen in protonated amine (equiv. to n+)

n3m
sp³ nitrogen in 3-membered ring (equiv. to na)

n3n
sp² nitrogen in 3-membered ring (equiv. to n)

n4m
sp³ nitrogen in 4-membered ring (equiv. to na)

n4n
sp² nitrogen in 4-membered ring (equiv. to n)

n+
protonated amine nitrogen

n=
nonaromatic end doubly bonded nitrogen

n=1
nonaromatic, next-to-end doubly bonded nitrogen

n=2
nonaromatic doubly bonded nitrogen

oxygen types

o
sp³ oxygen in alcohol, ether, acid, or ester group

oc
sp³ oxygen in ether or acetal (equiv. to o)

oe
sp³ oxygen in ester (equiv. to o)

oh
oxygen bonded to H (equiv. to o)

op
oxygen in aromatic ring (e.g., furan)

o3e
sp³ oxygen in 3-membered ring (equiv. to o)

o4e
sp³ oxygen in 4-membered ring (equiv. to o)

o´
oxygen in carbonyl (C=O) group

o*
oxygen in water

o-
oxygen in carboxylate (COO^-) group

sulfur types

s
sp³ sulfur in sulfide, disulfide, or thiol group

sc
sp³ sulfur in methionine (C-S-C) group (equiv. to s)

sh
sulfur in sulfhydryl (SH) group (equiv. to s)

sp
sulfur in aromatic ring (e.g., thiophene)

s1
sulfur involved in S-S disulfide bond (equiv. to s)

s3e
sulfur in 3-membered ring (equiv. to s)

s4e
sulfur in 4-membered ring (equiv. to s)

s´
sulfur in thioketone (>C=S) group

s-
partial-double sulfur bonded to something that is bonded to another partial-double oxygen or sulfur

phosphorus

p
general phosphorous atom

halogen types

br
bromine bonded to a carbon

cl
chlorine bonded to a carbon

f
fluorine bonded to a carbon

i
covalently bound iodine

ion types

Br
bromide ion

ca+
calcium ion (Ca²⁺)

Cl
chloride ion

Na
sodium ion

argon

ar
argon atom

silicon

si
silicon atom

other

lp
lone pair

nu
null atom for relative free energy

Table 27 . Atom types--CFF91 (Page 1 of 4)
general class	atom type	description
hydrogen types
	dw	deuterium in heavy water (equiv. to h*)
	h	hydrogen bonded to C or S
	hc	hydrogen bonded to C (equiv. to h)
	hi	hydrogen in charged imidazole ring
	hn	hydrogen bonded to N (equiv. to h*)
	ho	hydrogen bonded to O (equiv. to h*)
	hp	hydrogen bonded to P (equiv. to h)
	hs	hydrogen bonded to S (equiv. to h)
	hw	hydrogen in water (equiv. to h*)
	h*	polar hydrogen bonded to N or O
	h+	charged hydrogen (in cation)
carbon types
	c	generic sp³ carbon
	ca	general amino acid alpha carbon (sp³) (equiv. to c)
	cg	sp³ alpha carbon in glycine (equiv. to c)
	ci	sp² aromatic carbon in charged imidazole ring (his⁺) (equiv. to cp)
	co	sp³ carbon in acetal (equiv. to c)
	coh	sp³ carbon in acetal with hydrogen (equiv. to c)
	cp	sp² aromatic carbon
	cr	carbon in guanidinium group (HN=C(NH₂)₂) (arg)
	cs	sp² carbon in 5-membered ring next to S (equiv. to cp)
	ct	sp carbon involved in triple bond
	c1	sp³ carbon bonded to 1 H, 3 heavy atoms (equiv. to c)
	c2	sp³ carbon bonded to 2 H's, 2 heavy atoms (equiv. to c)
	c3	sp³ carbon in methyl (CH₃) group (equiv. to c)
	c5	sp² aromatic carbon in 5-membered ring (equiv. to cp)
	c3h	sp³ carbon in 3-membered ring with hydrogens (equiv. to c)
	c3m	sp³ carbon in 3-membered ring (equiv. to c)
	c4h	sp³ carbon in 4-membered ring with hydrogens (equiv. to c)
	c4m	sp³ carbon in 4-membered ring (equiv. to c)
	c´	sp² carbon in carbonyl (C=O) group in amide
	c"	carbon in carbonyl group, not amide (equiv. to c*)
	c*	carbon in carbonyl group, not amide
	c-	carbon in carboxylate (COO^-) group
	c+	carbon in guanidinium group
	c=	nonaromatic end doubly bonded carbon
	c=1	nonaromatic, next-to-end doubly bonded carbon
	c=2	nonaromatic doubly bonded carbon
nitrogen types
	n	sp² amide nitrogen
	na	sp³ amine nitrogen
	nb	sp² nitrogen in aromatic amine (equiv. to nn)
	nh	sp² nitrogen in 5- or 6-membered ring, bonded to hydrogen
	nho	sp² nitrogen in 6-membered ring, next to a carbonyl group and with a hydrogen (equiv. to nh)
	nh+	protonated nitrogen in 6-membered ring
	ni	sp² nitrogen in charged imidazole ring (his⁺) (equiv. to nh)
	nn	sp² nitrogen in aromatic amine
	np	sp² nitrogen in 5- or 6-membered ring, not bonded to hydrogen
	npc	sp² nitrogen in 5- or 6-membered ring, bonded to a heavy atom (equiv. to nh)
	nr	sp² nitrogen in guanidinium group (HN=C(NH₂)₂)
	nt	sp nitrogen involved in triple bond
	nz	sp nitrogen in N₂
	n1	sp² nitrogen in charged arginine (equiv. to nr)
	n2	sp² nitrogen in guanidinium group (HN=C(NH₂)₂) (equiv. to nr)
	n4	sp³ nitrogen in protonated amine (equiv. to n+)
	n3m	sp³ nitrogen in 3-membered ring (equiv. to na)
	n3n	sp² nitrogen in 3-membered ring (equiv. to n)
	n4m	sp³ nitrogen in 4-membered ring (equiv. to na)
	n4n	sp² nitrogen in 4-membered ring (equiv. to n)
	n+	protonated amine nitrogen
	n=	nonaromatic end doubly bonded nitrogen
	n=1	nonaromatic, next-to-end doubly bonded nitrogen
	n=2	nonaromatic doubly bonded nitrogen
oxygen types
	o	sp³ oxygen in alcohol, ether, acid, or ester group
	oc	sp³ oxygen in ether or acetal (equiv. to o)
	oe	sp³ oxygen in ester (equiv. to o)
	oh	oxygen bonded to H (equiv. to o)
	op	oxygen in aromatic ring (e.g., furan)
	o3e	sp³ oxygen in 3-membered ring (equiv. to o)
	o4e	sp³ oxygen in 4-membered ring (equiv. to o)
	o´	oxygen in carbonyl (C=O) group
	o*	oxygen in water
	o-	oxygen in carboxylate (COO^-) group
sulfur types
	s	sp³ sulfur in sulfide, disulfide, or thiol group
	sc	sp³ sulfur in methionine (C-S-C) group (equiv. to s)
	sh	sulfur in sulfhydryl (SH) group (equiv. to s)
	sp	sulfur in aromatic ring (e.g., thiophene)
	s1	sulfur involved in S-S disulfide bond (equiv. to s)
	s3e	sulfur in 3-membered ring (equiv. to s)
	s4e	sulfur in 4-membered ring (equiv. to s)
	s´	sulfur in thioketone (>C=S) group
	s-	partial-double sulfur bonded to something that is bonded to another partial-double oxygen or sulfur
phosphorus
	p	general phosphorous atom
halogen types
	br	bromine bonded to a carbon
	cl	chlorine bonded to a carbon
	f	fluorine bonded to a carbon
	i	covalently bound iodine
ion types
	Br	bromide ion
	ca+	calcium ion (Ca²⁺)
	Cl	chloride ion
	Na	sodium ion
argon
	ar	argon atom
silicon
	si	silicon atom
other
	lp	lone pair
	nu	null atom for relative free energy

CHARMm atom types

Table 28 . Atom types--CHARMm (Page 1 of 4)

general class atom type description
hydrogen types

H
hydrogen bonding hydrogen (neutral group)

HA
aliphatic or aromatic hydrogen

HC
hydrogen bonding hydrogen (charged group)

HMU
mu-bonded hydrogen for metals and boron-hydride

HO
hydrogen on an alcohol oxygen

HT
TIPS3P water-model hydrogen

carbon types

C
carbonyl or guanidinium carbon

C3
carbonyl carbon in 3-membered aliphatic ring

C4
carbonyl carbon in 4-membered aliphatic ring

C5R
aromatic carbon in 5-membered ring

C5RP
for aryl-aryl bond between C5R rings

C5RQ
for second aryl-aryl bond between C5RP rings (ortho)

C6R
aromatic carbon in a 6-membered ring

C6RP
for aryl-aryl bond between C6R rings

C6RQ
carbon of C6RP type ortho to C6RP pair

CF1
carbon with one fluorine

CF2
carbon with two fluorines

CF3
carbons with three fluorines

CM
carbon in carbon monoxide or other triply bonded carbon

CP3
carbon on nitrogen in proline ring

CPH1
CG and CD2 carbons in histidine ring

CPH2
CE1 carbon in histidine ring

CQ66
third adjacent pair of CR66 types in fused rings

CT
aliphatic carbon (tetrahedral)

CT3
carbon in 3-membered aliphatic ring, usually tetrahedral

CT4
carbon in 4-membered aliphatic ring, usually tetrahedral

CUA1
carbon in double bond, first pair

CUA2
carbon in double bond, second conjugated pair

CUA3
carbon in double bond, third conjugated pair

CUY1
carbon in triple bond, first pair

CUY2
carbon in triple bond, second conjugated pair

extended-atom carbon types

C5RE
extended aromatic carbon in 5-membered ring

C6RE
extended aromatic carbon in 6-membered ring

CH1E
extended-atom carbon with one hydrogen

CH2E
extended-atom carbon with two hydrogens

CH3E
extended-atom carbon with three hydrogens

CR55
aromatic carbon-merged 5-membered rings

CR56
aromatic carbon-merged 5- or 6-membered rings

CR66
aromatic carbon-merged 6-membered rings

CS66
second adjacent pair of CR66 types in fused rings

nitrogen types

N
nitrogen: planar-valence of 3, i.e., nitrile, etc.

N3
nitrogen in a 3-membered ring

N5R
nitrogen in a 5-membered aromatic ring

N5RP
for aryl-aryl bond between 5-membered rings

N6R
nitrogen in a 6-membered aromatic ring

N6RP
for aryl-aryl bond between 6-membered rings

NC
charged guanidinium-type nitrogen

NC2
for neutral guanidinium group - Arg sidechain

NO2
nitrogen in nitro or related group

NP
nitrogen in peptide, amide, or related group

NR1
protonated nitrogen in neutral histidine ring

NR2
unprotonated nitrogen in neutral histidine ring

NR3
nitrogens in charged histidine ring

NR55
N at fused bond between two 5-membered aromatics

NR56
N at fused bond between 5- and 6-membered aryls

NR66
N at fused bond between two 6-membered aromatics

NT
nitrogen (tetrahedral), i.e., amine, etc.

NX
proline nitrogen or similar

oxygen types

O
carbonyl oxygen for amide or related structures

O2M
oxygen in Si-O-Al or Al-O-Al bond

O5R
oxygen in 5-membered aromatic ring-radicals, etc.

O6R
oxygen in 6-membered aromatic ring-radicals, etc.

OA
carbonyl oxygen for aldehydes or related

OAC
carbonyl oxygen for acids or related

OC
charged oxygen

OE
ether oxygen / acetal oxygen

OH2
ST2 water-model oxygen

OK
carbonyl oxygen for ketones or related

OM
oxygen in carbon monoxide or other triply bonded oxygen

OS
ester oxygen

OSH
massless O for zeolites or related cage compounds

OSI
oxygen in Si-O-Si bond

OT
hydroxyl oxygen (tetrahedral) or ionizable acid

OW
TIP3P water-model oxygen

sulfur types

S5R
sulfur in a 5-membered aromatic ring

S6R
sulfur in a 6-membered aromatic ring

SE
thioether sulfur

SH1E
extended-atom sulfur with one hydrogen

SK
thioketone sulfur

SO1
sulfur bonded to one oxygen

SO2
sulfur bonded to two oxygens

SO3
sulfur bonded to three oxygens

SO4
sulfur bonded to four oxygens

ST
sulfur, general: usually tetrahedral

phosphorus types

P6R
phosphorous in aromatic 6-membered ring

PO3
phosphorous bonded to three oxygens

PO4
phosphorous bonded to four oxygens

PT
phosphorous, general: usually tetrahedral

PUA1
double-bonded phosphorous

PUY1
triple-bonded phosphorus

other

LP
ST2 lone pair

Table 28 . Atom types--CHARMm (Page 1 of 4)
general class	atom type	description
hydrogen types
	H	hydrogen bonding hydrogen (neutral group)
	HA	aliphatic or aromatic hydrogen
	HC	hydrogen bonding hydrogen (charged group)
	HMU	mu-bonded hydrogen for metals and boron-hydride
	HO	hydrogen on an alcohol oxygen
	HT	TIPS3P water-model hydrogen
carbon types
	C	carbonyl or guanidinium carbon
	C3	carbonyl carbon in 3-membered aliphatic ring
	C4	carbonyl carbon in 4-membered aliphatic ring
	C5R	aromatic carbon in 5-membered ring
	C5RP	for aryl-aryl bond between C5R rings
	C5RQ	for second aryl-aryl bond between C5RP rings (ortho)
	C6R	aromatic carbon in a 6-membered ring
	C6RP	for aryl-aryl bond between C6R rings
	C6RQ	carbon of C6RP type ortho to C6RP pair
	CF1	carbon with one fluorine
	CF2	carbon with two fluorines
	CF3	carbons with three fluorines
	CM	carbon in carbon monoxide or other triply bonded carbon
	CP3	carbon on nitrogen in proline ring
	CPH1	CG and CD2 carbons in histidine ring
	CPH2	CE1 carbon in histidine ring
	CQ66	third adjacent pair of CR66 types in fused rings
	CT	aliphatic carbon (tetrahedral)
	CT3	carbon in 3-membered aliphatic ring, usually tetrahedral
	CT4	carbon in 4-membered aliphatic ring, usually tetrahedral
	CUA1	carbon in double bond, first pair
	CUA2	carbon in double bond, second conjugated pair
	CUA3	carbon in double bond, third conjugated pair
	CUY1	carbon in triple bond, first pair
	CUY2	carbon in triple bond, second conjugated pair
extended-atom carbon types
	C5RE	extended aromatic carbon in 5-membered ring
	C6RE	extended aromatic carbon in 6-membered ring
	CH1E	extended-atom carbon with one hydrogen
	CH2E	extended-atom carbon with two hydrogens
	CH3E	extended-atom carbon with three hydrogens
	CR55	aromatic carbon-merged 5-membered rings
	CR56	aromatic carbon-merged 5- or 6-membered rings
	CR66	aromatic carbon-merged 6-membered rings
	CS66	second adjacent pair of CR66 types in fused rings
nitrogen types
	N	nitrogen: planar-valence of 3, i.e., nitrile, etc.
	N3	nitrogen in a 3-membered ring
	N5R	nitrogen in a 5-membered aromatic ring
	N5RP	for aryl-aryl bond between 5-membered rings
	N6R	nitrogen in a 6-membered aromatic ring
	N6RP	for aryl-aryl bond between 6-membered rings
	NC	charged guanidinium-type nitrogen
	NC2	for neutral guanidinium group - Arg sidechain
	NO2	nitrogen in nitro or related group
	NP	nitrogen in peptide, amide, or related group
	NR1	protonated nitrogen in neutral histidine ring
	NR2	unprotonated nitrogen in neutral histidine ring
	NR3	nitrogens in charged histidine ring
	NR55	N at fused bond between two 5-membered aromatics
	NR56	N at fused bond between 5- and 6-membered aryls
	NR66	N at fused bond between two 6-membered aromatics
	NT	nitrogen (tetrahedral), i.e., amine, etc.
	NX	proline nitrogen or similar
oxygen types
	O	carbonyl oxygen for amide or related structures
	O2M	oxygen in Si-O-Al or Al-O-Al bond
	O5R	oxygen in 5-membered aromatic ring-radicals, etc.
	O6R	oxygen in 6-membered aromatic ring-radicals, etc.
	OA	carbonyl oxygen for aldehydes or related
	OAC	carbonyl oxygen for acids or related
	OC	charged oxygen
	OE	ether oxygen / acetal oxygen
	OH2	ST2 water-model oxygen
	OK	carbonyl oxygen for ketones or related
	OM	oxygen in carbon monoxide or other triply bonded oxygen
	OS	ester oxygen
	OSH	massless O for zeolites or related cage compounds
	OSI	oxygen in Si-O-Si bond
	OT	hydroxyl oxygen (tetrahedral) or ionizable acid
	OW	TIP3P water-model oxygen
sulfur types
	S5R	sulfur in a 5-membered aromatic ring
	S6R	sulfur in a 6-membered aromatic ring
	SE	thioether sulfur
	SH1E	extended-atom sulfur with one hydrogen
	SK	thioketone sulfur
	SO1	sulfur bonded to one oxygen
	SO2	sulfur bonded to two oxygens
	SO3	sulfur bonded to three oxygens
	SO4	sulfur bonded to four oxygens
	ST	sulfur, general: usually tetrahedral
phosphorus types
	P6R	phosphorous in aromatic 6-membered ring
	PO3	phosphorous bonded to three oxygens
	PO4	phosphorous bonded to four oxygens
	PT	phosphorous, general: usually tetrahedral
	PUA1	double-bonded phosphorous
	PUY1	triple-bonded phosphorus
other
	LP	ST2 lone pair

COMPASS atom types

Table 29 . Atom types--COMPASS (Page 1 of 5)

general class atom type description
hydrogen types

h
hydrogen, generic

h1
hydrogen, nonpolar

h1+
hydrogen, proton

h1h
hydrogen in H₂

h1n
hydrogen bound to N, Cl

h1o
hydrogen bound to O, F

carbon types

c
carbon, generic

c1o
carbon in carbon monoxide, CO

c2=
carbon, SP, two double bonds O=C=O, S=C=S

c2t
carbon, SP, triple bond

c3
carbon, SP2, generic, 3 bonds

c3"
carbon, SP2, carbonyl, two polar substituents

c3#
carbon, SP2, in CO₃^2- anion

c3'
carbon, SP2, carbonyl, one polar substituent

c3-
carbon, SP2, carboxylate

c3=
carbon, SP2, double bond to C (-C=C-)

c3a
carbon, SP2, aromatic

c3n
carbon, SP2, double bond to N (-C=N-)

c3o
carbon, SP2, carbonyl

c4
carbon, SP3, generic, 4 bonds

c43
carbon, SP3, with 3 heavy atoms

c44
carbon, SP3, with 4 heavy atoms

c4o
carbon, SP3, bond to oxygen

c4x
carbon, SP3, bond to chlorine

nitrogen types

n
nitrogen, generic

n1n
nitrogen, in N₂

n1o
nitrogen in NO

n1t
nitrogen, SP, 1 triple bond

n2=
nitrogen, SP2, 1 double bond, non-aromatic

n2a
nitrogen, SP2, 2 partial double bonds, aromatic

n2t
nitrogen, SP, 1 triple bond, non-aromatic

n3
nitrogen, SP3, in amines

n3*
nitrogen, SP3, in NH₃

n3+
nitrogen, SP3, charged

n3a
nitrogen, SP2, aromatic

n3h1
nitrogen, SP3, in amines with 1 hydrogen

n3h2
nitrogen, SP3, in amines with 2 hydrogens

n3m
nitrogen, SP3, in amides without hydrogen

n3mh
nitrogen, SP3, in amides with hydrogen

n3o
nitrogen, SP2, in nitro group

n4+
nitrogen, SP3, in protonated amine

n4o
nitrogen, SP3, in amine oxide

oxygen types

o
oxygen, generic

o-2
oxygen, anion in metal oxides (O^-2)

o1-
oxygen, SP2, in carboxylate

o12
oxygen, SP2, in nitro group (-NO₂)

o1=
oxygen, SP2, in carbonyl

o1=*
oxygen, in CO₂

o1c
oxygen, in CO

o1n
oxygen, in NO

o1o
oxygen, in O₂

o2
oxygen, SP3, generic

o2*
oxygen, SP3, in water

o2a
oxygen, SP2, aromatic, in 5-membered ring

o2b
oxygen, SP3, bridge atom in anhydrides

o2c
oxygen, SP3, in acids

o2e
oxygen, SP3, in ethers

o2h
oxygen, SP3, in alcohol

o2s
oxygen, SP3, in esters

o2z
oxygen, in siloxanes and zeolites

o3
oxygen, in H₃O⁺

o3z
oxygen, bridge in zeolites

sulfur types

s
sulfur, generic

s1=
sulfur, 1 double bond (=S)

s2
sulfur, 2 single bonds (-S-)

s2=
sulfur, 2 double bonds (=S=)

s2a
sulfur, in aromatic ring (thiophene)

s3=
sulfur, 3 bonds, 1 is double

s4
sulfur, 4 single bonds

s4=
sulfur, 4 bonds, 2 are double

s6
sulfur, 6 single bonds

phosphorus types

p
phosphorus, generic

p4=
phosphorus, in phosphazenes

halogen types

br
bromine, generic

br-
bromine, anion

br1
bromine, one bond

cl
chlorine, generic

cl-
chlorine anion

cl1
chlorine, one bond

cl12
chlorine, to a carbon that has 2 X

cl13
chlorine, to a carbon that has 3 X

cl14
chlorine, to a carbon that has 4 X

cl1p
chlorine, in phosphazenes

f
fluorine, generic

f-
fluorine anion

f1
fluorine, one bond

f12
fluorine, to a carbon that has 2 F

f13
fluorine, to a carbon that has 3 F

f14
fluorine, to a carbon that has 4 F

f1p
fluorine, in phosphazene

i
iodine, generic

i-
iodine anion

i1
iodine, with one bond

metal types

Ag
silver, metal

Al
aluminum, metal

Au
gold, metal

Cr
chromium, metal

Cu
copper, metal

Fe
iron, metal

Mo
molybdenum, metal

Ni
nickel, metal

Pb
lead, metal

Pd
palladium, metal

Pt
platinum, metal

Sn
tin, metal

W
tungsten, metal

metal ion types

ca+
calcium ion (Ca²⁺)

cu+2
copper ion (Cu²⁺)

fe+2
iron ion (Fe²⁺)

mg+2
magnesium ion (Mg²⁺)

zn+2
zinc ion (Zn²⁺)

alkali metal and ion types

K
potassium, metal

Li
lithium, metal

Na
sodium, metal

cs+
cesium ion (Cs⁺)

k+
potassium ion (K⁺)

li+
lithium ion (Li⁺)

na+
sodium ion (Na⁺)

rb+
rubidium ion (Rb+)

zeolite and silicon types

al4z
aluminum, in zeolites

si
silicon, generic

si4
silicon, generic with 4 bonds

si4c
silicon, in siloxane with heavy atoms only

si4z
silicon, in zeolites

noble gas types

ar
argon

he
helium

kr
krypton

ne
neon

xe
xenon

Table 29 . Atom types--COMPASS (Page 1 of 5)
general class	atom type	description
hydrogen types
	h	hydrogen, generic
	h1	hydrogen, nonpolar
	h1+	hydrogen, proton
	h1h	hydrogen in H₂
	h1n	hydrogen bound to N, Cl
	h1o	hydrogen bound to O, F
carbon types
	c	carbon, generic
	c1o	carbon in carbon monoxide, CO
	c2=	carbon, SP, two double bonds O=C=O, S=C=S
	c2t	carbon, SP, triple bond
	c3	carbon, SP2, generic, 3 bonds
	c3"	carbon, SP2, carbonyl, two polar substituents
	c3#	carbon, SP2, in CO₃^2- anion
	c3'	carbon, SP2, carbonyl, one polar substituent
	c3-	carbon, SP2, carboxylate
	c3=	carbon, SP2, double bond to C (-C=C-)
	c3a	carbon, SP2, aromatic
	c3n	carbon, SP2, double bond to N (-C=N-)
	c3o	carbon, SP2, carbonyl
	c4	carbon, SP3, generic, 4 bonds
	c43	carbon, SP3, with 3 heavy atoms
	c44	carbon, SP3, with 4 heavy atoms
	c4o	carbon, SP3, bond to oxygen
	c4x	carbon, SP3, bond to chlorine
nitrogen types
	n	nitrogen, generic
	n1n	nitrogen, in N₂
	n1o	nitrogen in NO
	n1t	nitrogen, SP, 1 triple bond
	n2=	nitrogen, SP2, 1 double bond, non-aromatic
	n2a	nitrogen, SP2, 2 partial double bonds, aromatic
	n2t	nitrogen, SP, 1 triple bond, non-aromatic
	n3	nitrogen, SP3, in amines
	n3*	nitrogen, SP3, in NH₃
	n3+	nitrogen, SP3, charged
	n3a	nitrogen, SP2, aromatic
	n3h1	nitrogen, SP3, in amines with 1 hydrogen
	n3h2	nitrogen, SP3, in amines with 2 hydrogens
	n3m	nitrogen, SP3, in amides without hydrogen
	n3mh	nitrogen, SP3, in amides with hydrogen
	n3o	nitrogen, SP2, in nitro group
	n4+	nitrogen, SP3, in protonated amine
	n4o	nitrogen, SP3, in amine oxide
oxygen types
	o	oxygen, generic
	o-2	oxygen, anion in metal oxides (O^-2)
	o1-	oxygen, SP2, in carboxylate
	o12	oxygen, SP2, in nitro group (-NO₂)
	o1=	oxygen, SP2, in carbonyl
	o1=*	oxygen, in CO₂
	o1c	oxygen, in CO
	o1n	oxygen, in NO
	o1o	oxygen, in O₂
	o2	oxygen, SP3, generic
	o2*	oxygen, SP3, in water
	o2a	oxygen, SP2, aromatic, in 5-membered ring
	o2b	oxygen, SP3, bridge atom in anhydrides
	o2c	oxygen, SP3, in acids
	o2e	oxygen, SP3, in ethers
	o2h	oxygen, SP3, in alcohol
	o2s	oxygen, SP3, in esters
	o2z	oxygen, in siloxanes and zeolites
	o3	oxygen, in H₃O⁺
	o3z	oxygen, bridge in zeolites
sulfur types
	s	sulfur, generic
	s1=	sulfur, 1 double bond (=S)
	s2	sulfur, 2 single bonds (-S-)
	s2=	sulfur, 2 double bonds (=S=)
	s2a	sulfur, in aromatic ring (thiophene)
	s3=	sulfur, 3 bonds, 1 is double
	s4	sulfur, 4 single bonds
	s4=	sulfur, 4 bonds, 2 are double
	s6	sulfur, 6 single bonds
phosphorus types
	p	phosphorus, generic
	p4=	phosphorus, in phosphazenes
halogen types
	br	bromine, generic
	br-	bromine, anion
	br1	bromine, one bond
	cl	chlorine, generic
	cl-	chlorine anion
	cl1	chlorine, one bond
	cl12	chlorine, to a carbon that has 2 X
	cl13	chlorine, to a carbon that has 3 X
	cl14	chlorine, to a carbon that has 4 X
	cl1p	chlorine, in phosphazenes
	f	fluorine, generic
	f-	fluorine anion
	f1	fluorine, one bond
	f12	fluorine, to a carbon that has 2 F
	f13	fluorine, to a carbon that has 3 F
	f14	fluorine, to a carbon that has 4 F
	f1p	fluorine, in phosphazene
	i	iodine, generic
	i-	iodine anion
	i1	iodine, with one bond
metal types
	Ag	silver, metal
	Al	aluminum, metal
	Au	gold, metal
	Cr	chromium, metal
	Cu	copper, metal
	Fe	iron, metal
	Mo	molybdenum, metal
	Ni	nickel, metal
	Pb	lead, metal
	Pd	palladium, metal
	Pt	platinum, metal
	Sn	tin, metal
	W	tungsten, metal
metal ion types
	ca+	calcium ion (Ca²⁺)
	cu+2	copper ion (Cu²⁺)
	fe+2	iron ion (Fe²⁺)
	mg+2	magnesium ion (Mg²⁺)
	zn+2	zinc ion (Zn²⁺)
alkali metal and ion types
	K	potassium, metal
	Li	lithium, metal
	Na	sodium, metal
	cs+	cesium ion (Cs⁺)
	k+	potassium ion (K⁺)
	li+	lithium ion (Li⁺)
	na+	sodium ion (Na⁺)
	rb+	rubidium ion (Rb+)
zeolite and silicon types
	al4z	aluminum, in zeolites
	si	silicon, generic
	si4	silicon, generic with 4 bonds
	si4c	silicon, in siloxane with heavy atoms only
	si4z	silicon, in zeolites
noble gas types
	ar	argon
	he	helium
	kr	krypton
	ne	neon
	xe	xenon

CVFF atom types

Table 30 . Atom types--CVFF (Page 1 of 4)

general class atom type description
hydrogen types

d
general deuterium (equiv. to h)

dw
deuterium in heavy water (equiv. to h)

h
generic hydrogen bonded to C, Si, or H

hc
hydrogen bonded to C (equiv. to h)

hi
hydrogen in charged imidazole ring (equiv. to hn)

hn
hydrogen bonded to N

ho
hydrogen bonded to O

hp
hydrogen bonded to P (equiv. to h)

hs
hydrogen bonded to S

hw
hydrogen in water (equiv. to h)

h*
hydrogen in water

h+
charged hydrogen in cation (equiv. to hn)

hscp
hydrogen in SPC water model

htip
hydrogen in TIP3P water model

carbon types

c
generic sp³ carbon

ca
general amino acid alpha carbon (sp³) (equiv. to cg)

cg
sp³ alpha carbon in glycine

ci
sp² aromatic carbon in charged imidazole ring (his⁺)

cn
sp³ carbon bonded to N (equiv. to cg)

co
sp³ carbon in acetal (equiv. to c)

coh
sp³ carbon in acetal with hydrogen (equiv. to cg)

cp
sp² aromatic carbon (partial double bonds)

cr
carbon in guanidinium group (HN=C(NH₂)₂) (arg)

cs
sp² carbon in 5-membered ring next to S

ct
sp carbon involved in triple bond

c1
sp³ carbon bonded to 1 H, 3 heavy atoms (equiv. to cg)

c2
sp³ carbon bonded to 2 H's, 2 heavy atoms (equiv. to cg)

c3
sp³ carbon in methyl (CH₃) group (equiv. to cg)

c5
sp² aromatic carbon in 5-membered ring

c3h
sp³ carbon in 3-membered ring with hydrogens (equiv. to cg)

c3m
sp³ carbon in 3-membered ring (equiv. to c)

c4h
sp³ carbon in 4-membered ring with hydrogens (equiv. to cg)

c4m
sp³ carbon in 4-membered ring (equiv. to c)

c´
sp² carbon in carbonyl (C=O) group of amide

c"
carbon in carbonyl group, not amide (equiv. to c´)

c*
carbon in carbonyl group, not amide (equiv. to c´)

c-
carbon in charged carboxylate (COO^-) group (equiv. to c´)

c+
carbon in guanidinium group (equiv. to cr)

c=
nonaromatic end doubly bonded carbon

c=1
nonaromatic, next-to-end doubly bonded carbon

c=2
nonaromatic doubly bonded carbon

nitrogen types

n
generic sp² nitrogen in amide

na
sp³ nitrogen in amine (equiv. to n3)

nb
sp² nitrogen in aromatic amine (equiv. to n3)

nh
sp² nitrogen in 5- or 6-membered ring, with hydrogen attached (equiv. to np)

nho
sp² nitrogen in 6-membered ring, next to a carbonyl group and with a hydrogen (equiv. to np)

nh+
protonated nitrogen in 6-membered ring

ni
sp² nitrogen in charged imidazole ring (his⁺)

nn
sp² nitrogen in aromatic amine (equiv. to n3)

np
sp² nitrogen in 5- or 6-membered ring

npc
sp² nitrogen in 5- or 6-membered ring, bonded to a heavy atom (equiv. to np)

nr
sp² nitrogen in guanidinium group (HN=C(NH₂)₂)

nt
sp nitrogen involved in triple bond

nz
sp nitrogen in N₂

n1
sp² nitrogen in charged arginine

n2
sp² nitrogen in guanidinium group (HN=C(NH₂)₂)

n3
sp³ nitrogen with 3 substituents

n4
sp³ nitrogen in protonated amine

n3m
sp³ nitrogen in 3-membered ring (equiv. to n3)

n3n
sp² nitrogen in 3-membered ring (equiv. to n)

n4m
sp³ nitrogen in 4-membered ring (equiv. to n3)

n4n
sp² nitrogen in 4-membered ring (equiv. to n)

n+
sp³ nitrogen in protonated amine (equiv. to n4)

n=
nonaromatic end doubly bonded nitrogen

n=1
nonaromatic, next-to-end doubly bonded nitrogen

n=2
nonaromatic doubly bonded nitrogen

oxygen types

o
generic sp³ oxygen

oc
sp³ oxygen in ether or acetal (equiv. to o)

oe
sp³ oxygen in ester (equiv. to o)

oh
oxygen bonded to H

op
sp² aromatic oxygen in 5-membered ring

o3e
sp³ oxygen in 3-membered ring (equiv. to o)

o4e
sp³ oxygen in 4-membered ring (equiv. to o)

o´
oxygen in carbonyl (C=O) group

o*
oxygen in water

o-
oxygen in charged carboxylate (COO^-) group

oscp
oxygen in SPC water model

otip
oxygen in TIP3P water model

sulfur types

s
sp³ sulfur

sc
sp³ sulfur in methionine (C-S-C) group (equiv. to s)

sh
sulfur in sulfhydryl (SH) group

sp
sulfur in aromatic ring, e.g., thiophene

s1
sulfur involved in S-S disulfide bond (equiv. to s)

s3e
sulfur in 3-membered ring (equiv. to s)

s4e
sulfur in 4-membered ring (equiv. to s)

s´
sulfur in thioketone (>C=S) group

s-
partial-double sulfur bonded to something that is bonded to another partial-double oxygen or sulfur

phosphorus

p
general phosphorous atom

halogen types

br
bromine bonded to a carbon

cl
chlorine bonded to a carbon

f
fluorine bonded to a carbon

i
covalently bound iodine

ion types

Br
bromide ion

ca+
calcium ion (Ca²⁺)

Cl
chloride ion

Na
sodium ion

argon

ar
argon atom

silicon

si
silicon atom

other

lp
lone pair

nu
null atom for relative free energy calculations

Table 30 . Atom types--CVFF (Page 1 of 4)
general class	atom type	description
hydrogen types
	d	general deuterium (equiv. to h)
	dw	deuterium in heavy water (equiv. to h*)
	h	generic hydrogen bonded to C, Si, or H
	hc	hydrogen bonded to C (equiv. to h)
	hi	hydrogen in charged imidazole ring (equiv. to hn)
	hn	hydrogen bonded to N
	ho	hydrogen bonded to O
	hp	hydrogen bonded to P (equiv. to h)
	hs	hydrogen bonded to S
	hw	hydrogen in water (equiv. to h*)
	h*	hydrogen in water
	h+	charged hydrogen in cation (equiv. to hn)
	hscp	hydrogen in SPC water model
	htip	hydrogen in TIP3P water model
carbon types
	c	generic sp³ carbon
	ca	general amino acid alpha carbon (sp³) (equiv. to cg)
	cg	sp³ alpha carbon in glycine
	ci	sp² aromatic carbon in charged imidazole ring (his⁺)
	cn	sp³ carbon bonded to N (equiv. to cg)
	co	sp³ carbon in acetal (equiv. to c)
	coh	sp³ carbon in acetal with hydrogen (equiv. to cg)
	cp	sp² aromatic carbon (partial double bonds)
	cr	carbon in guanidinium group (HN=C(NH₂)₂) (arg)
	cs	sp² carbon in 5-membered ring next to S
	ct	sp carbon involved in triple bond
	c1	sp³ carbon bonded to 1 H, 3 heavy atoms (equiv. to cg)
	c2	sp³ carbon bonded to 2 H's, 2 heavy atoms (equiv. to cg)
	c3	sp³ carbon in methyl (CH₃) group (equiv. to cg)
	c5	sp² aromatic carbon in 5-membered ring
	c3h	sp³ carbon in 3-membered ring with hydrogens (equiv. to cg)
	c3m	sp³ carbon in 3-membered ring (equiv. to c)
	c4h	sp³ carbon in 4-membered ring with hydrogens (equiv. to cg)
	c4m	sp³ carbon in 4-membered ring (equiv. to c)
	c´	sp² carbon in carbonyl (C=O) group of amide
	c"	carbon in carbonyl group, not amide (equiv. to c´)
	c*	carbon in carbonyl group, not amide (equiv. to c´)
	c-	carbon in charged carboxylate (COO^-) group (equiv. to c´)
	c+	carbon in guanidinium group (equiv. to cr)
	c=	nonaromatic end doubly bonded carbon
	c=1	nonaromatic, next-to-end doubly bonded carbon
	c=2	nonaromatic doubly bonded carbon
nitrogen types
	n	generic sp² nitrogen in amide
	na	sp³ nitrogen in amine (equiv. to n3)
	nb	sp² nitrogen in aromatic amine (equiv. to n3)
	nh	sp² nitrogen in 5- or 6-membered ring, with hydrogen attached (equiv. to np)
	nho	sp² nitrogen in 6-membered ring, next to a carbonyl group and with a hydrogen (equiv. to np)
	nh+	protonated nitrogen in 6-membered ring
	ni	sp² nitrogen in charged imidazole ring (his⁺)
	nn	sp² nitrogen in aromatic amine (equiv. to n3)
	np	sp² nitrogen in 5- or 6-membered ring
	npc	sp² nitrogen in 5- or 6-membered ring, bonded to a heavy atom (equiv. to np)
	nr	sp² nitrogen in guanidinium group (HN=C(NH₂)₂)
	nt	sp nitrogen involved in triple bond
	nz	sp nitrogen in N₂
	n1	sp² nitrogen in charged arginine
	n2	sp² nitrogen in guanidinium group (HN=C(NH₂)₂)
	n3	sp³ nitrogen with 3 substituents
	n4	sp³ nitrogen in protonated amine
	n3m	sp³ nitrogen in 3-membered ring (equiv. to n3)
	n3n	sp² nitrogen in 3-membered ring (equiv. to n)
	n4m	sp³ nitrogen in 4-membered ring (equiv. to n3)
	n4n	sp² nitrogen in 4-membered ring (equiv. to n)
	n+	sp³ nitrogen in protonated amine (equiv. to n4)
	n=	nonaromatic end doubly bonded nitrogen
	n=1	nonaromatic, next-to-end doubly bonded nitrogen
	n=2	nonaromatic doubly bonded nitrogen
oxygen types
	o	generic sp³ oxygen
	oc	sp³ oxygen in ether or acetal (equiv. to o)
	oe	sp³ oxygen in ester (equiv. to o)
	oh	oxygen bonded to H
	op	sp² aromatic oxygen in 5-membered ring
	o3e	sp³ oxygen in 3-membered ring (equiv. to o)
	o4e	sp³ oxygen in 4-membered ring (equiv. to o)
	o´	oxygen in carbonyl (C=O) group
	o*	oxygen in water
	o-	oxygen in charged carboxylate (COO^-) group
	oscp	oxygen in SPC water model
	otip	oxygen in TIP3P water model
sulfur types
	s	sp³ sulfur
	sc	sp³ sulfur in methionine (C-S-C) group (equiv. to s)
	sh	sulfur in sulfhydryl (SH) group
	sp	sulfur in aromatic ring, e.g., thiophene
	s1	sulfur involved in S-S disulfide bond (equiv. to s)
	s3e	sulfur in 3-membered ring (equiv. to s)
	s4e	sulfur in 4-membered ring (equiv. to s)
	s´	sulfur in thioketone (>C=S) group
	s-	partial-double sulfur bonded to something that is bonded to another partial-double oxygen or sulfur
phosphorus
	p	general phosphorous atom
halogen types
	br	bromine bonded to a carbon
	cl	chlorine bonded to a carbon
	f	fluorine bonded to a carbon
	i	covalently bound iodine
ion types
	Br	bromide ion
	ca+	calcium ion (Ca²⁺)
	Cl	chloride ion
	Na	sodium ion
argon
	ar	argon atom
silicon
	si	silicon atom
other
	lp	lone pair
	nu	null atom for relative free energy calculations

CVFF_aug atom types

As in CVFF (Table 30) with these additional atom types:

Table 31 . Atom types--CVFF_aug (Page 1 of 3)
element	atom type	charge	description
Si	sz	2.4	tetrahedral silicon in a zeolite or silicate
O	oz	-1.2	oxygen in a zeolite or silicate
Al	az	1.4	tetrahedral aluminum atom in zeolites
P	pz	3.4	phosphorous atom in zeolites
Ga	ga	1.4	gallium atom in zeolites
Ge	ge	2.4	germanium atom in zeolites
Ti	tioc	1.6	titanium (octahedral) in zeolites
Ti	titd	2.4	titanium (tetrahedral) in zeolites
Li	li+	1.0	lithium ion in zeolites
Na	na+	1.0	sodium ion in zeolites
K	k+	1.0	potassium ion in zeolites
Rb	rb+	1.0	rubidium ion in zeolites
Cs	cs+	1.0	cesium ion in zeolites
Mg	mg2+	2.0	magnesium ion in zeolites
Ca	ca2+	2.0	calcium ion in zeolites
Ba	ba2+	2.0	barium ion in zeolites
Cu	cu2+	2.0	copper(II) ion in zeolites
F	f-	-1.0	fluoride ion in zeolites
Cl	cl-	-1.0	chloride ion in zeolites
Br	br-	-1.0	bromide ion in zeolites
I	i-	-1.0	iodide ion in zeolites
S	so4	2.8	sulfur in sulfate ion to be used with oz

Si	sy	4.0	tetrahedral silicon atom in clays
O	oy	-2.0	oxygen atom in clays
Al	ay	3.0	octahedral aluminum atom in clays
Al	ayt	3.0	tetrahedral aluminum atom to be used with oy
Na	nac+	1.0	sodium ion in clays
Mg	mg2c	2.0	octahedral magnesium ion in clays
Fe	fe2c	2.0	octahedral Fe(II) ion in clays
Mn	mn4c	4.0	manganese (IV) ion to be used with oy
Mn	mn3c	3.0	manganese (III) ion to be used with oy
Co	co2c	2.0	cobalt (II) ion to be used with oy
Ni	ni2c	2.0	nickel (II) ion to be used with oy
Li	lic+	1.0	lithium ion to be used with oy
Pd	pd2+	2.0	palladium(II)
Ti	ti4c	4.0	titanium (octahedral) to be used with oy
Sr	sr2c	2.0	strontium ion to be used with oy
Ca	ca2c	2.0	calcium ion to be used with oy
Cl	cly-	-1.0	chloride ion to be used with oy
H	hocl	1.0	hydrogen in hydroxyl group in clays
P	py	5.0	phosphorous atom to be used with oy
V	vy	4.0	tetrahedral vanadium to be used with oy
N	nh4+	1.0	united-atom type for ammonium ion to be used with oy
S	so4y	6.0	sulfur in sulfate ion to be used with oy
Li	lioh	1.0	lithium ion in water to be used with o*
Na	naoh	1.0	sodium ion in water to be used with o*
K	koh	-1.0	potassium ion in water to be used with o*
F	foh	-1.0	fluoride ion in water to be used with o*
Cl	cloh	-1.0	chloride ion in water to be used with o*
Be	beoh	0.0	beryllium (II) in water to be used with o*
Al	al	0.0	aluminum metal
Na	Na	0.0	sodium metal
Pt	Pt	0.0	platinum metal
Pd	Pd	0.0	palladium metal
Au	Au	0.0	gold metal
Ag	Ag	0.0	silver metal
Sn	Sn	0.0	tin metal
K	K	0.0	potassium metal
Li	Li	0.0	lithium metal
Mo	Mn	0.0	molybdenum metal
Fe	Fe	0.0	iron metal
W	W	0.0	tungsten metal
Ni	Ni	0.0	nickel metal
Cr	Cr	0.0	chromium metal
Cu	Cu	0.0	copper metal
Pb	Pb	0.0	lead metal

ESFF atom types

The atom types in ESFF for the first three rows of the periodic table are listed in Table 32. For the atom types that are not listed in Table 32, please refer to the $BIOSYM_LIBRARY/esff.frc file.

Atom-typing rules in ESFF

The names of the atom types for metals are based on the symmetry of the metal complex and on both the oxidation state and coordination number of the metal. For example, Ag024t indicates an Ag that has an oxidation level of 2+, is 4-coordinated, and has tetrahedral symmetry. The following table lists the abbreviations used for the symmetry types:

symbol symmetry
l
C_2v

s
D_4h

t
T_d

o
O_h

p
D_5h

h
D_2h, D_3h

d
D

symbol	symmetry
l	C_2v
s	D_4h
t	T_d
o	O_h
p	D_5h
h	D_2h, D_3h
d	D

Some metals with differing oxidation numbers and symmetries may be handled with the same parameters. Here, a generic metal atom type is used.

The oxidation number of a metal is determined according to:

Eq. 136

where Q_t is the total charge on the complex, and the sums over Fq_i and Fq_j are the sums of formal charges on atoms not bonded to metals and bonded to metals, respectively. N_m is the number of metal atoms in the complex, and N_b is the number of metal atoms bonded to the jth ligand atom.

Table 32 Atom types for the first three rows¹ of the periodic table--ESFF (Page 1 of 5)
general class	atom type	description
hydrogen types
	dw	deuterium in heavy water
	h	generic hydrogen
	hi	hydrogen in charged imidazole ring (equiv. to h*)
	hw	hydrogen in water (equiv. to h*)
	h*	hydrogen bonded to nitrogen, oxygen
	h+	charged hydrogen in cations
carbon types
	c	generic sp³ carbon
	ca	general amino acid alpha carbon (sp3) (equiv. to c)
	cg	sp³ alpha carbon in glycine (equiv. to c)
	ci	carbon in charged imidazole ring (equiv. to cp)
	co	sp³ carbon in acetals (equiv. to c)
	coh	sp³ carbon in acetals with hydrogen (equiv. to c)
	cp	sp² aromatic carbon with partial double bond
	cr	c in neutral arginine (equiv. to c=)
	cs	sp² aromatic carbon in 5-membered ring next to S (equiv. to cp)
	ct	sp carbon involved in a triple bond
	ct3	sp carbon involved in CO
	c1	sp³ carbon with 1 H 3 heavies (equiv. to c)
	c2	sp³ carbon with 2 H's, 2 heavies (equiv. to c)
	c3	sp³ carbon with 3 H's, 1 heavy (equiv. to c)
	c5	sp² aromatic carbon in 5-membered ring
	c5p	sp² aromatic carbon in 5-membered big pi ring
	c'	carbon in carbonyl (C=O) group
	c-	c in charged carboxylate
	c+	c in guanidinium group (equiv. to c=)
	c=	generic sp² carbon
nitrogen types
	n	generic sp² nitrogen (in amides)
	na	sp³ nitrogen in amines
	nb	sp² nitrogen in aromatic amines
	nh	sp² (3 [sp²] 2 [p]) nitrogen in 5-membered ring
	nho	sp² nitrogen in 6-membered ring
	ni	nitrogen in charged imidazole ring (equiv. to nh)
	no	sp² nitrogen in oxides of nitrogen
	np	sp² nitrogen in 5-membered ring
	nt	sp nitrogen involved in a triple bond
	nt2	central nitrogen involved in azide group
	nz	sp nitrogen in N2
	n1	sp² nitrogen in charged arginine (equiv. to n=)
	n2	sp² nitrogen (NH₂) in guanidinium group (HN=C(NH₂)₂) (equiv. to n=)
	n4	sp³ nitrogen with 4 substituents (equiv. to n+)
	n+	sp³ nitrogen in protonated amines
	n=	sp² nitrogen in neutral arginine (double bond)
oxygen types
	o	generic sp³ oxygen in alcohol, ether, or acid group
	oa	sp³ oxygen in ester or acid
	oc	sp³ oxygen in ether or acetalsE (equiv. to o)
	oh	oxygen bonded to hydrogen (equiv. to o)
	op	sp² aromatic in 5-membered ring
	os	oxygen bonded to two silicons
	ot	oxygen with hybridization sp
	o1	oxygen bonded to oxygen
	o'	oxygen having a single double bond
	o*	oxygen in water
	o-	double bonded oxygen in charged carboxylate COO^- (equiv. to o')
sulfur types
	s	sp³ sulfur
	sp	sulfur in an aromatic ring (e.g., thiophene)
	s1	sp³ sulfur involved in (S-S) group of disulfides
	s2d	sulfur with oxidation number 4, two double sigma bond
	s3d	sulfur with oxidation number 4, three sigma bond, (C_3v)
	s4d	sulfur with oxidation number 6, four sigma bond, (T_d)
	s4l	sulfur with coordination number 4 (C_2v)
	s5l	sulfur with coordination number 5 (D_4h, C_2v)
	s5t	sulfur with coordination number 5 (D_3h)
	s6	sulfur with coordination number 6 (D_4h, D_2h)
	s6o	sulfur with coordination number 6 (O_h)
	s'	S in thioketone group
	s-	double bonded sulfur in charged phosphate PSS^- or PSO^- (equiv. to s')
phosphorus types
	p	general phosphorous atom
	p4d	phosphorous atom with oxidation number 5 and 4 sigma bonds (C_Td)
	p4l	phosphorous atom with oxidation number 5 and 3 sigma bonds (C_2v)
	p5l	phosphorous atom with oxidation number 5 and 3 sigma bonds (D_4h, C_2v)
	p5t	phosphorous atom with oxidation number 5 and 3 sigma bonds (D_3h)
	p53	phosphorous atom with oxidation number 5 and 3 sigma bonds (planar)
	p6	phosphorous atom with oxidation number 5 and 3 sigma bonds (D_4h, D_2h)
	p6o	phosphorous atom with oxidation number 5 and 3 sigma bonds (O_h)
	p'	sp² phosphorous atom
other second-row elements
	b	boron sp³ atom
	bt	boron sp atom
	b'	boron sp² atom
	Be	berillium atom
	Be+	berillium cation
	Be+2	berillium cation
	f	fluorine atom
	F	fluorine anion
	Li	lithium atom with s orbitals involved in bonding
	Li+	lithium ion
	ne	neon atom
other third-row elements
	ar	argon atom
	Al	aluminum atom
	Al033	aluminum atom with coordination number 3
	Al034	aluminum atom with coordination number 4
	Al035	aluminum atom with coordination number 5
	Al035s	aluminum atom with coordination number 5 (D_4h)
	Al035t	aluminum atom with coordination number 5 (D_3h)
	Al036	aluminum atom with coordination number 6 (D_4h, D_2h)
	Al036o	aluminum atom with coordination number 6 (O_h)
	cl	chlorine atom
	Cl	chlorine ion
	cl'	chlorine atom in oxo acid
	he	helium atom
	Mg	magnesium atom
	Mg025	magnesium atom with 5 coordinations
	Mg025s	magnesium atom with 5 coordinations (D_4h)
	Mg025t	magnesium atom with 5 coordinations (D_3h)
	Mg026	magnesium atom with 6 coordinations (D_4h, D_2h)
	Mg026o	magnesium atom with 6 coordinations
	Mg+	magnesium +1 cation (O_h)
	Mg+2	magnesium +2 cation
	Na	sodium atom
	Na+	sodium ion
	si	silicon atom
	si4l	silicon atom (D_3h, C_2v)
	si5l	silicon atom (D_4h)
	si5t	silicon atom (D_3h)
	si6	silicon atom (D_4h, D_2h)
	si6o	silicon atom (O_h)
	si'	sp² silicon atom

PCFF--additional atom types

This table lists those atom types included in PCFF in addition to the CFF91 atom types listed in Table 27.

Table 33 . Additional atom types--PCFF¹ (Page 1 of 2)

general class atom type description
hydrogen types

hn2
amino hydrogen

ho2
hydroxyl hydrogen

carbonyl functional groups (C and O)

c_0
carbonyl carbon of aldehydes, ketones

c_1
carbonyl carbon of acid, ester, amide

c_2
carbonyl carbon of carbamate, urea

cz
carbonyl carbon of carbonate

o=
oxygen double bonded to O, C, S, N, P

o_1
oxygen in carbonyl group

o_2
ester oxygen

oo
oxygen in carbonyl group, carbonate only

oz
ester oxygen in carbonate

phosphorus types

p=
phosphazene phosphorous atom

silicon-related types

si
silicon atom

sio
siloxane silicon

hsi
silane hydrogen

osi
siloxane oxygen

noble gas types

he
helium

ar
argon

kr
krypton

ne
neon

xe
xenon

metal atoms and halogen ions

Ag
silver metal

Al
aluminium metal

Au
gold metal

Br
bromine ion

Cl
chlorine ion

Cr
chromium metal

Cu
copper metal

Fe
iron metal

K
potassium metal

Li
lithium metal

Mo
molybdenum metal

Na
sodium metal

Ni
nickel metal

Pb
lead metal

Pd
palladium metal

Pt
platinum metal

Sn
tin metal

W
tungsten metal

zeolite-related types

az
aluminium atom in zeolites

oss
oxygen atom betweem two silicons

osh
oxygen atom in terminal hydroxyl group on silicon

oah
oxygen atom in terminal hydroxyl group on aluminium

oas
oxygen atom between aluminium and silicon

ob
oxygen atom in bridging hydroxyl group

sz
silicon atom in zeolites

hb
hydrogen atom in bridging hydroxyl group

hoa
hydrogen atom in terminal hydroxyl group on aluminium

hos
hydrogen atom in terminal hydroxyl group on silicon

¹ PCFF also includes all the atom types listed for CFF91 (page 285).

Table 33 . Additional atom types--PCFF¹ (Page 1 of 2)
general class	atom type	description
hydrogen types
	hn2	amino hydrogen
	ho2	hydroxyl hydrogen
carbonyl functional groups (C and O)
	c_0	carbonyl carbon of aldehydes, ketones
	c_1	carbonyl carbon of acid, ester, amide
	c_2	carbonyl carbon of carbamate, urea
	cz	carbonyl carbon of carbonate
	o=	oxygen double bonded to O, C, S, N, P
	o_1	oxygen in carbonyl group
	o_2	ester oxygen
	oo	oxygen in carbonyl group, carbonate only
	oz	ester oxygen in carbonate
phosphorus types
	p=	phosphazene phosphorous atom
silicon-related types
	si	silicon atom
	sio	siloxane silicon
	hsi	silane hydrogen
	osi	siloxane oxygen
noble gas types
	he	helium
	ar	argon
	kr	krypton
	ne	neon
	xe	xenon
metal atoms and halogen ions
	Ag	silver metal
	Al	aluminium metal
	Au	gold metal
	Br	bromine ion
	Cl	chlorine ion
	Cr	chromium metal
	Cu	copper metal
	Fe	iron metal
	K	potassium metal
	Li	lithium metal
	Mo	molybdenum metal
	Na	sodium metal
	Ni	nickel metal
	Pb	lead metal
	Pd	palladium metal
	Pt	platinum metal
	Sn	tin metal
	W	tungsten metal
zeolite-related types
	az	aluminium atom in zeolites
	oss	oxygen atom betweem two silicons
	osh	oxygen atom in terminal hydroxyl group on silicon
	oah	oxygen atom in terminal hydroxyl group on aluminium
	oas	oxygen atom between aluminium and silicon
	ob	oxygen atom in bridging hydroxyl group
	sz	silicon atom in zeolites
	hb	hydrogen atom in bridging hydroxyl group
	hoa	hydrogen atom in terminal hydroxyl group on aluminium
	hos	hydrogen atom in terminal hydroxyl group on silicon

Last updated September 04, 1998 at 12:14PM Pacific Daylight Time.

Table 24 . Common potential terms in major forcefields supported by MSI

AMBER atom types

Table 25 . Atom types--AMBER (Page 1 of 4)

Table 26 . Atom types--Homans

Table 27 . Atom types--CFF91 (Page 1 of 4)

Table 28 . Atom types--CHARMm (Page 1 of 4)

Table 29 . Atom types--COMPASS (Page 1 of 5)

Table 30 . Atom types--CVFF (Page 1 of 4)

CVFF_aug atom types

Table 31 . Atom types--CVFF_aug (Page 1 of 3)

ESFF atom types

Eq. 136

Table 32 Atom types for the first three rows1 of the periodic table--ESFF (Page 1 of 5)

PCFF--additional atom types

Table 33 . Additional atom types--PCFF1 (Page 1 of 2)

Table 32 Atom types for the first three rows¹ of the periodic table--ESFF (Page 1 of 5)

Table 33 . Additional atom types--PCFF¹ (Page 1 of 2)