amber_old_to_new.map

! equivalences between new amber atom types and old (parm94) atom types
! from parm99.dat
LP      Cl     #lone pair
HZ      HC     #H bond sp C (Howard et al.JCC,16,243,1995)

! from frcmod.ionsff99_tip3p
Li+     Li     #lithium   pol: J. Phys. Chem. 11,1541,(1978)
Na+     Na     #sodium    pol: J. Phys. Chem. 11,1541,(1978)
K+      K      #potassium
Rb+     Rb     #rubidium
Cs+     Cs     #cesium
F-      F      #fluorine
Cl-     Cl     #chlorine  (Applequist)
Br-     Br     #bromine   (Applequist)
I-      I      #iodine    (Applequist)

! from parm10.dat
CI      CT     #parmbsc0
CP      CK     #sp2 C 5 memb.ring in purines (G)
CS      CM     #sp2 C pyrimidines in pos. 5 & 6 (U)
CX      CT     #protein C-alpha (new to ff10)    # copied from parm10   #GLYCAM_06j.dat
C5      CK     #sp2 C 5 memb.ring in purines (A)
C4      CM     #sp2 C pyrimidines in pos. 5 & 6 (C)
OP      O2     #2- phosphate oxygen

! from frcmod.parmbsc0_ezOL1
C3      CT     #sp3 aliphatic C

! from frcmod.parmbsc1
CE      CT
C1      CK     #sp2 C purines in pos. 8 Ade (CK)
C2      CM     #sp2 C pyrimidines in pos. 5 & 6 Thy Ura (CM)

! from parm15ipq_10.3.dat
CO      C      #sp2 C carboxylate group
2C      CT     #sp3 aliphatic C with two (duo) heavy atoms   # copied from ff12SB   #GLYCAM_06j.dat
3C      CT     #sp3 aliphatic C with three (tres) heavy atoms  # copied from ff12SB   #GLYCAM_06j.dat
C8      CT     #sp3 aliphatic C basic AA side chain
OD      O      #ASN/GLN amide O; backbone
ND      N      #ASN/GLN amide O; NHE
OA      OH     #SER/THR/TYR hydroxyl O
NL      N3     #LYS ammonium N; backbone N-terminus
TN      NT     #PRO backbone N
TJ      CT     #PRO backbone CA
TG      CT     #GLY backbone CA
TP      CT     #ARG/HIP/LYS backbone CA
TM      CT     #ASP/CYM/GLU backbone CA
TH      H      #ARG nitrogen-attached H
TA      CT     #HID/HIE/PHE/TRP/TYR CB

! from GLYCAM_06j.dat
Cg      CT     #sp3 C aliphatic
Cy      CT     #sp3 C aliphatic - for sialic acid only!
Cp      CT     #sp3 C aliphatic - carbon atom bonded to an oxygen atom bonded to a phosphorus atom
Ck      CD     #sp2 C alkenes
Cj      CD     #sp2 C alkenes for adjacent double bonds
Ng      N      #sp2 N amide group
Oh      OH     #O hydroxyl group
Os      OS     #O ether
Oy      OS     #O ether - for sialic acid only!
Sm      S      #sulfane carbohydrate linkage (-CH2-S-CH2-)
Hc      HC     #H aliph. bond. to C without electrwd. groups
Ha      HC     #H aliph. bond. to C in alkenes eg Ck
Ho      HO     #H hydroxyl group
Hp      HP     #H bonded to C next to positively charged group

! from gaff.dat
c       C      #Sp2 C carbonyl group
c1      CZ     #Sp C
c2      CD     #Sp2 C
c3      CT     #Sp3 C
ca      CA     #Sp2 C in pure aromatic systems
cp      CA     #Head Sp2 C that connect two rings in biphenyl sys.
cq      CA     #Head Sp2 C that connect two rings in biphenyl sys. identical to cp
cc      CC     #Sp2 carbons in non-pure aromatic systems
cd      CC     #Sp2 carbons in non-pure aromatic systems, identical to cc
ce      CD     #Inner Sp2 carbons in conjugated systems
cf      CD     #Inner Sp2 carbons in conjugated systems, identical to ce
cg      CZ     #Inner Sp carbons in conjugated systems
ch      CZ     #Inner Sp carbons in conjugated systems, identical to cg
cx      CT     #Sp3 carbons in triangle systems
cy      CT     #Sp3 carbons in square systems
cu      CD     #Sp2 carbons in triangle systems
cv      CD     #Sp2 carbons in square systems
cz      CA     #Sp2 carbon in guanidine group
h1      H1     #H bonded to aliphatic carbon with 1 electrwd. group
h2      H2     #H bonded to aliphatic carbon with 2 electrwd. group
h3      H3     #H bonded to aliphatic carbon with 3 electrwd. group
h4      H4     #H bonded to non-sp3 carbon with 1 electrwd. group
h5      H5     #H bonded to non-sp3 carbon with 2 electrwd. group
ha      HA     #H bonded to aromatic carbon
hc      HC     #H bonded to aliphatic carbon without electrwd. group
hn      H      #H bonded to nitrogen atoms
ho      HO     #Hydroxyl group
hp      HP     #H bonded to phosphate
hs      HS     #Hydrogen bonded to sulphur
hw      HW     #Hydrogen in water
hx      HP     #H bonded to C next to positively charged group
f       F      #Fluorine
cl      Cl     #Chlorine
br      Br     #Bromine
i       I      #Iodine
n       N      #Sp2 nitrogen in amide groups
n1      NY     #Sp N
n2      N2     #aliphatic Sp2 N with two connected atoms
n3      NT     #Sp3 N with three connected atoms
n4      N3     #Sp3 N with four connected atoms
na      NA     #Sp2 N with three connected atoms
nb      NB     #Sp2 N in pure aromatic systems
nc      NC     #Sp2 N in non-pure aromatic systems
nd      NC     #Sp2 N in non-pure aromatic systems, identical to nc
ne      NA     #Inner Sp2 N in conjugated systems
nf      NA     #Inner Sp2 N in conjugated systems, identical to ne
nh      NT     #Amine N connected one or more aromatic rings
no      NT     #Nitro N
ni      NT     #n in 3-memberred rings       #like n in RG3          #gaff2.dat
nj      NT     #n in 4-memberred rings       #like n in RG4          #gaff2.dat
nk      NT     #n4 in 3-memberred rings      #like n4/nx/ny in RG3   #gaff2.dat
nl      NT     #n4 in 4-memberred rings      #like n4/nx/ny in RG4   #gaff2.dat
nm      NT     #nh in 3-memberred rings      #like nh in RG3         #gaff2.dat
nn      NT     #nh in 4-memberred rings      #like nh in RG4         #gaff2.dat
np      NT     #n3 in 3-memberred rings      #like n3 in RG3         #gaff2.dat
nq      NT     #n3 in 4-memberred rings      #like n3 in RG4         #gaff2.dat
o       O      #Oxygen with one connected atom
oh      OH     #Oxygen in hydroxyl group
oq      OS     #os in 4-memberred rings
os      OS     #Ether and ester oxygen
op      OS     #os in 3-memberred rings
ow      OW     #Oxygen in water
p2      P      #Phosphate with two connected atoms
p3      P      #Phosphate with three connected atoms, such as PH3
p4      P      #Phosphate with three connected atoms, such as O=P(CH3)2
p5      P      #Phosphate with four connected atoms, such as O=P(OH)3
pb      P      #Sp2 P in pure aromatic systems
pc      P      #Sp2 P in non-pure aromatic systems
pd      P      #Sp2 P in non-pure aromatic systems, identical to pc
pe      P      #Inner Sp2 P in conjugated systems
pf      P      #Inner Sp2 P in conjugated systems, identical to pe
px      P      #Special p4 in conjugated systems
py      P      #Special p5 in conjugated systems
s       S      #S with one connected atom
s2      S      #S with two connected atom, involved at least one double bond
s4      S      #S with three connected atoms
s6      S      #S with four connected atoms
sh      SH     #Sp3 S connected with hydrogen
sp      S      #ss in 3-memberred rings
sq      S      #ss in 4-memberred rings
ss      S      #Sp3 S in thio-ester and thio-ether
sx      S      #Special s4 in conjugated systems
sy      S      #Special s6 in conjugated systems

! from gaff2.dat
cs      C      #Sp2 C in c=S
ns      NT     #amind N, with 1 attached hydrogen atom
nt      N      #amide N, with 2 attached hydrogen atoms
nx      N3     #like n4, but only has one hydrogen atom
ny      N3     #like n4, but only has two hydrogen atoms
nz      N3     #like n4, but only has three three hydrogen atoms
n+      N3     #NH4+
nu      NT     #like nh, but only has one attached hydrogen atom
nv      NT     #like nh, but only has two attached hydrogen atoms
n5      NT     #like n7 in RG3
n6      NT     #like n7 in RG4
n7      NT     #like n3, but only has one attached hydrogen atom
n8      NT     #like n3, but only has two attached hydrogen atoms
n9      NT     #NH3