LyX Document

Type	Element	Hybridization	Defined in	Used in parm	Used in prep	Used in lib/off	Used for
2C	C	sp3	leaprc.ff12SB	frcmod.ff12SB	amino12.in	amino12.lib	sp3 amino acid side chain carbon bonded to 2 heavy atoms
3C	C	sp3	leaprc.ff12SB	frcmod.ff12SB	amino12.in	amino12.lib	sp3 amino acid side chain carbon bonded to 3 heavy atoms
AC	C	sp3	leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
BR	Br	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
Br	Br	sp3	leaprc.ff10
			leaprc.ff12SB
br	Br	sp3	leaprc.gaff
Br-	Br	sp3	leaprc.ff10
			leaprc.ff12SB
C	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep	GLYCAM_amino.lib	Carbonyl carbon
			leaprc.GLYCAM_06EP*	GLYCAM_06EP*.dat	GLYCAM_06EP*.prep		Carbonyl carbon
			leaprc.pol12
c	C	sp2	leaprc.gaff
C*	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
C0	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
C1	C	sp2	leaprc.parmCHI_YIL.bsc
		sp3	leaprc.ff03ua
c1	C	sp2	leaprc.gaff
C2	C	sp2	leaprc.parmCHI_YIL.bsc
		sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
c2	C	sp2	leaprc.gaff
C3	C	sp2	leaprc.parmCHI_YIL.bsc
		sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
c3	C	sp3	leaprc.gaff
C4	C	sp2	leaprc.ff10
			leaprc.ff12SB
			leaprc.parmCHI_YIL.bsc
		sp3	leaprc.ff99SBildn
C5	C	sp2	leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99SBildn
C6	C	sp2	leaprc.ff99SBildn
C8	C	sp3	leaprc.ff12SB	frcmod.ff12SB	amino12.in	amino12.lib	sp3 carbon in lysine and arginine side chains
CA	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.ffPM3
			leaprc.pol12
			leaprc.pol12
cA	C	sp3	leaprc.lipid11
ca	C	sp2	leaprc.gaff
CB	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
cB	C	sp2	leaprc.lipid11
CC	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
cC	C	sp2	leaprc.lipid11
cc	C	sp2	leaprc.gaff
CD	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
cd	C	sp2	leaprc.gaff
CE	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
ce	C	sp2	leaprc.gaff
CF	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
cf	C	sp2	leaprc.gaff
CG	C	sp3	leaprc.GLYCAM_06	GLYCAM_06[a-g].dat	GLYCAM_06.prep GLYCAM_06_lipids.prep	GLYCAM_amino.lib	Glycan carbon
			leaprc.GLYCAM_06EP	GLYCAM_06EPa.dat	GLYCAM_06EPa.prep		Glycan carbon
Cg	C	sp3	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep GLYCAM_lipids_06h.prep	GLYCAM_amino*_06h.lib	Glycan carbon
			leaprc.GLYCAM_06EPb	GLYCAM_06EPb.dat	GLYCAM_06EPb.prep		Glycan carbon
cg	C	sp2	leaprc.gaff
CH	C	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
ch	C	sp2	leaprc.gaff
CI	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
		sp3	leaprc.ff10
			leaprc.ff12SB
			leaprc.parmCHI_YIL.bsc
CJ	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB	n/a
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06	GLYCAM_06[a-g].dat	GLYCAM_06.prep	GLYCAM_06_amino*.lib	Alkenes with adjacent double bonds
			leaprc.pol12
Cj	C	sp2	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep	GLYCAM_amino*_06h.lib	Alkenes with adjacent double bonds
CK	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06	GLYCAM_06[a-g].dat	GLYCAM_06.prep	GLYCAM_06_amino*.lib
			leaprc.pol12
Ck	C	sp2	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep	GLYCAM_amino*_06h.lib	Alkenes
CL	Cl	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
Cl	Cl	sp3	leaprc.ff10
			leaprc.ff12SB
cl	Cl	sp3	leaprc.gaff
Cl-	Cl	sp3	leaprc.ff10
			leaprc.ff12SB
CM	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
CN	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
CO	C	sp2	leaprc.ff12SB	frcmod.ff12SB	amino12.in	amino12.lib	sp2 oxygen bound to two O2 in Asp and Glu side chains
CP	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
		sp3	leaprc.GLYCAM_06	GLYCAM_06[a-g].dat	GLYCAM_06.prep GLYCAM_06_lipids.prep	GLYCAM_06_amino*.lib	sp3 C - sp3 O - sp3 P
Cp	C	sp3	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep GLYCAM_lipids_06h.prep	GLYCAM_amino*_06h.lib	sp3 C - sp3 O - sp3 P
cP	C	sp3	leaprc.lipid11
cp	C	sp2	leaprc.gaff
CQ	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
cq	C	sp2	leaprc.gaff
CR	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
cR	C	sp3	leaprc.lipid11
CS	C	sp2	leaprc.ff10
			leaprc.ff12SB
Cs	Cs	sp3	leaprc.ff02pol.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.pol12
Cs+	Cs	sp3	leaprc.ff10
			leaprc.ff12SB
CT	C	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep (not lipids)	GLYCAM_amino.lib	non-glycan aliphatic C
			leaprc.pol12
cu	C	sp2	leaprc.gaff
CV	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
cv	C	sp2	leaprc.gaff
CW	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
CX	C	sp3	leaprc.ff10	parm10.dat	amino10.in	amino10.lib	Amino acid α carbon
			leaprc.ff12SB
cx	C	sp2	leaprc.gaff
CY	C	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
		sp3	leaprc.GLYCAM_06	GLYCAM_06[a-g].dat	GLYCAM_06.prep	GLYCAM_06_amino*.lib	sialic acid
Cy	C	sp3	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep	GLYCAM_amino*_06h.lib	sialic acid
cy	C	sp2	leaprc.gaff
EC	C	sp3	leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
EP		sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06EP*	GLYCAM_06EP*.dat	GLYCAM_06EP*.prep		extra points (lone pairs)
			leaprc.pol12
F	F	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
f	F	sp3	leaprc.gaff
F-	F	sp3	leaprc.ff10
			leaprc.ff12SB
FE	Fe	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
H	H	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep (not lipids)	GLYCAM_amino.lib	H bonded to nitrogen atoms
			leaprc.GLYCAM_06EP*	GLYCAM_06EP*.dat	GLYCAM_06EP*.prep		H bonded to nitrogen atoms
			leaprc.pol12
H0	H	sp3	leaprc.ff02pol.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.pol12
H1	H	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep	GLYCAM_amino.lib	Aliphatic H bonded to a C with 1 electron withdrawing group
			leaprc.GLYCAM_06EP*	GLYCAM_06EP*.dat	GLYCAM_06EP*.prep		Aliphatic H bonded to a C with 1 electron withdrawing group
			leaprc.pol12
h1	H	sp3	leaprc.gaff
H2	H	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep (not lipids)	GLYCAM_amino.lib	Aliphatic H bonded to a C with 2 electron withdrawing groups
			leaprc.GLYCAM_06EP*	GLYCAM_06EP*.dat	GLYCAM_06EP*.prep		Aliphatic H bonded to a C with 2 electron withdrawing groups
			leaprc.pol12
h2	H	sp3	leaprc.gaff
H3	H	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
h3	H	sp3	leaprc.gaff
H4	H	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
h4	H	sp3	leaprc.gaff
H5	H	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
h5	H	sp3	leaprc.gaff
HA	H	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06	GLYCAM_06[a-g].dat	GLYCAM_06.prep	GLYCAM_06_amino*.lib	Aliphatic H bonded to a C in an alkene (e.g., CK or Ck)
			leaprc.pol12
Ha	H	sp3	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep	GLYCAM_amino*_06h.lib	Aliphatic H bonded to a C in an alkene (e.g., CK or Ck)
hA	H	sp3	leaprc.lipid11
ha	H	sp3	leaprc.gaff
hB	H	sp3	leaprc.lipid11
HC	H	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06	GLYCAM_06[a-g].dat	GLYCAM_06.prep GLYCAM_06_lipids.prep	GLYCAM_06_amino*.lib	Aliphatic H bonded to a C without electron withdrawing groups
			leaprc.GLYCAM_06EPb	GLYCAM_06EPb.dat	GLYCAM_06EPb.prep		Aliphatic H bonded to a C without electron withdrawing groups
			leaprc.pol12
Hc	H	sp3	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep GLYCAM_lipids_06h.prep	GLYCAM_amino*_06h.lib	Aliphatic H bonded to a C without electron withdrawing groups
			leaprc.GLYCAM_06EPb	GLYCAM_06EPb.dat	GLYCAM_06EPb.prep		Aliphatic H bonded to a C without electron withdrawing groups
hc	H	sp3	leaprc.gaff
hE	H	sp3	leaprc.lipid11
hN	H	sp3	leaprc.lipid11
hn	H	sp3	leaprc.gaff
HO	H	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
			leaprc.GLYCAM_06	GLYCAM_06[a-g].dat	GLYCAM_06.prep	GLYCAM_06_amino*.lib	Hydroxyl hydrogen
			leaprc.GLYCAM_06EP	GLYCAM_06EPa.dat	GLYCAM_06EPa.prep		Hydroxyl hydrogen
Ho	H	sp3	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep	GLYCAM_amino*_06h.lib	Hydroxyl hydrogen in a glycan
			leaprc.GLYCAM_06EPb	GLYCAM_06EPb.dat	GLYCAM_06EPb.prep		Hydroxyl hydrogen in a glycan
hO	H	sp3	leaprc.lipid11
ho	H	sp3	leaprc.gaff
HP	H	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06	GLYCAM_06[a-g].dat	GLYCAM_06.prep GLYCAM_06_lipids.prep	GLYCAM_06_amino*.lib	H bonded C next to a positively charged group
			leaprc.pol12
Hp	H	sp3	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep GLYCAM_lipids_06h.prep	GLYCAM_amino*_06h.lib	H bonded C next to a positively charged group
hp	H	sp3	leaprc.gaff
hR	H	sp3	leaprc.lipid11
HS	H	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
hS	H	sp3	leaprc.lipid11
hs	H	sp3	leaprc.gaff
HW	H	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep (not lipids)	GLYCAM_amino.lib	Hydrogen in water
			leaprc.GLYCAM_06EP*	GLYCAM_06EP*.dat	GLYCAM_06EP*.prep		Hydrogen in water
			leaprc.pol12
hw	H	sp3	leaprc.gaff
hX	H	sp3	leaprc.lipid11
hx	H	sp3	leaprc.gaff
HZ	H	sp3	leaprc.ff10
			leaprc.ff12SB
I	I	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
i	I	sp3	leaprc.gaff
I-	I	sp3	leaprc.ff10
			leaprc.ff12SB
IB	Na	sp3	leaprc.ff02pol.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.pol12
IM	Cl	sp3	leaprc.ff02pol.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.pol12
IP	Na	sp3	leaprc.ff02pol.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.pol12
K	K	sp3	leaprc.ff02pol.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.pol12
K+	K	sp3	leaprc.ff10
			leaprc.ff12SB
Li	Li	sp3	leaprc.ff02pol.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.pol12
Li+	Li	sp3	leaprc.ff10
			leaprc.ff12SB
LP		sp3	leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
MG	Mg	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
Mg+	Mg	sp3	leaprc.ff10
			leaprc.ff12SB
N	N	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep (not lipids)	GLYCAM_amino.lib	sp2 N amide group
			leaprc.pol12
n	N	sp2	leaprc.gaff
N*	N	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
n1	N	sp2	leaprc.gaff
N2	N	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
n2	N	sp2	leaprc.gaff
N3	N	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep	GLYCAM_amino.lib	sp3 N for charged amino acid groups
			leaprc.pol12
n3	N	sp3	leaprc.gaff
n4	N	sp3	leaprc.gaff
NA	N	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
nA	N	sp3	leaprc.lipid11
na	N	sp2	leaprc.gaff
Na+	Na	sp3	leaprc.ff10
			leaprc.ff12SB
NB	N	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
nb	N	sp2	leaprc.gaff
NC	N	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
nc	N	sp2	leaprc.gaff
nd	N	sp2	leaprc.gaff
ne	N	sp2	leaprc.gaff
nf	N	sp2	leaprc.gaff
Ng	N	sp2	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep	GLYCAM_amino*_06h.lib	Glycan sp2 amide
nh	N	sp2	leaprc.gaff
no	N	sp2	leaprc.gaff
NP	N	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
NQ	N	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
NT	N	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep	GLYCAM_amino.lib	sp3 N amine group
			leaprc.pol12
NY	N	sp2	leaprc.ff10
			leaprc.ff12SB
O	O	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep	GLYCAM_amino.lib	O in a carbonyl group
			leaprc.GLYCAM_06EP*	GLYCAM_06EP*.dat	GLYCAM_06EP*.prep		O in a carbonyl group
			leaprc.pol12
o	O	sp2	leaprc.gaff
O2	O	sp2	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep	GLYCAM_amino.lib	O in a carboxyl group
			leaprc.GLYCAM_06EP*	GLYCAM_06EP*.dat	GLYCAM_06EP*.prep		O in a carboxyl group
			leaprc.pol12
o2	O	sp2	leaprc.gaff
Oa	N	sp2	leaprc.GLYCAM_12	GLYCAM_12.dat	GLYCAM_12.prep	GLYCAM_amino*_12.lib	Glycan sp2 nitrogen
oC	O	sp2	leaprc.lipid11
Oe	N	sp2	leaprc.GLYCAM_12	GLYCAM_12.dat	GLYCAM_12.prep	GLYCAM_amino*_12.lib	Glycan sp2 nitrogen
OG	O	sp3	leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
OH	O	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06	GLYCAM_06[a-g].dat	GLYCAM_06.prep	GLYCAM_06_amino*.lib	Hydroxyl oxygen
			leaprc.GLYCAM_06EP	GLYCAM_06EPa.dat	GLYCAM_06EPa.prep		Hydroxyl oxygen
			leaprc.pol12
Oh	O	sp3	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep	GLYCAM_amino*_06h.lib	Hydroxyl oxygen in a glycan
			leaprc.GLYCAM_06EPb	GLYCAM_06EPb.dat	GLYCAM_06EPb.prep		Hydroxyl oxygen in a glycan
oH	O	sp3	leaprc.lipid11
oh	O	sp3	leaprc.gaff
OL	O	sp3	leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
OM	O	sp2	leaprc.ff99SBildn
oO	O	sp2	leaprc.lipid11
OP	O	sp2	leaprc.ff10
			leaprc.ff12SB
oP	O	sp2	leaprc.lipid11
oR	O	sp3	leaprc.lipid11
OS	O	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06	GLYCAM_06[a-g].dat	GLYCAM_06.prep GLYCAM_06_lipids.prep	GLYCAM_06_amino*.lib	Ether Oxygen
			leaprc.GLYCAM_06EP	GLYCAM_06EPa.dat	GLYCAM_06EPa.prep		Ether Oxygen
			leaprc.pol12
Os	O	sp3	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep GLYCAM_lipids_06h.prep	GLYCAM_amino*_06h.lib	Ether Oxygen
			leaprc.GLYCAM_06EPb	GLYCAM_06EPb.dat	GLYCAM_06EPb.prep		Ether Oxygen
oS	O	sp3	leaprc.lipid11
os	O	sp3	leaprc.gaff
oT	O	sp3	leaprc.lipid11
OW	O	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep	GLYCAM_amino.lib	Water oxygen
			leaprc.GLYCAM_06EP*	GLYCAM_06EP*.dat	GLYCAM_06EP*.prep		Water oxygen
			leaprc.pol12
ow	O	sp3	leaprc.gaff
OY	O	sp3	leaprc.GLYCAM_06	GLYCAM_06[a-g].dat	GLYCAM_06.prep	GLYCAM_06_amino*.lib	sialic acid
Oy	O	sp3	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep	GLYCAM_amino*_06h.lib	sialic acid
P	P	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep	GLYCAM_amino.lib	phosphorus in phosphates
			leaprc.pol12
p2	P	sp2	leaprc.gaff
p3	P	sp3	leaprc.gaff
p4	P	sp3	leaprc.gaff
p5	P	sp3	leaprc.gaff
pA	P	sp3	leaprc.lipid11
pb	P	sp3	leaprc.gaff
pd	P	sp3	leaprc.gaff
px	P	sp3	leaprc.gaff
py	P	sp3	leaprc.gaff
Rb	Rb	sp3	leaprc.ff02pol.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.pol12
Rb+	Rb	sp3	leaprc.ff10
			leaprc.ff12SB
S	S	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.GLYCAM_06*	GLYCAM_06*.dat	GLYCAM_06*.prep (not lipids)	GLYCAM_amino.lib	sulfur in sulfates
			leaprc.pol12
s	S	sp2	leaprc.gaff
s2	S	sp2	leaprc.gaff
s3	S	sp3	leaprc.gaff
s4	S	sp3	leaprc.gaff
s6	S	sp3	leaprc.gaff
SH	S	sp3	leaprc.ff02pol.r1
			leaprc.ff02polEP.r1
			leaprc.ff03.r1
			leaprc.ff03ua
			leaprc.ff10
			leaprc.ff12SB
			leaprc.ff99bsc0
			leaprc.ff99SB
			leaprc.ff99SBildn
			leaprc.ff99SBnmr
			leaprc.ffAM1
			leaprc.ffPM3
			leaprc.pol12
sh	S	sp3	leaprc.gaff
SM	S	sp3	leaprc.GLYCAM_06	GLYCAM_06[a-g].dat	GLYCAM_06.prep	GLYCAM_06_amino*.lib	Sulfane in a carbohydrate linkage
Sm	S	sp3	leaprc.GLYCAM_06h	GLYCAM_06h.dat	GLYCAM_06h.prep	GLYCAM_amino*_06h.lib	Sulfane in a carbohydrate linkage
ss	S	sp3	leaprc.gaff
sx	S	sp3	leaprc.gaff
sy	S	sp3	leaprc.gaff
Zn	Zn	sp3	leaprc.ff02pol.r1