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atomtypes.atp
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Br 79.90000 ; bromine
C 12.01000 ; sp2 C carbonyl group
CA 12.01000 ; sp2 C pure aromatic (benzene)
CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction
CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS
CK 12.01000 ; sp2 C 5 memb.ring in purines
CM 12.01000 ; sp2 C pyrimidines in pos. 5 & 6
CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
CQ 12.01000 ; sp2 C in 5 mem.ring of purines between 2 N
CR 12.01000 ; sp2 arom as CQ but in HIS
CT 12.01000 ; sp3 aliphatic C
CV 12.01000 ; sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)
CW 12.01000 ; sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
C* 12.01000 ; sp2 arom. 5 memb.ring w/1 subst. (TRP)
C0 40.08000 ; calcium
F 19.00000 ; fluorine
H 1.00800 ; H bonded to nitrogen atoms
HQ 1.00800 ; new amber99sb-ucb,ASN,GLN,LYN(neutral LYS) added at 09.07.2020
HC 1.00800 ; H aliph. bond. to C without electrwd.group
H1 1.00800 ; H aliph. bond. to C with 1 electrwd. group
H2 1.00800 ; H aliph. bond. to C with 2 electrwd.groups
H3 1.00800 ; H aliph. bond. to C with 3 eletrwd.groups
HA 1.00800 ; H arom. bond. to C without elctrwd. groups
H4 1.00800 ; H arom. bond. to C with 1 electrwd. group
H5 1.00800 ; H arom. bond. to C with 2 electrwd. groups
HO 1.00800 ; hydroxyl group
HS 1.00800 ; hydrogen bonded to sulphur (pol?)
HW 1.00800 ; H in TIP3P water
HP 1.00800 ; H bonded to C next to positively charged gr
I 126.90000 ; iodine (Applequist)
Cl 35.45000 ; chlorine (Applequist)
Na 22.99000 ; Na+, ions pol:J.PhysC,11,1541,(1978)
IB 131.00000 ; 'big ion w/ waters' for vacuum (Na+, 6H2O)
MG 24.30500 ; magnesium
N 14.01000 ; sp2 nitrogen in amide groups
NA 14.01000 ; sp2 N in 5 memb.ring w/H atom (HIS)
NB 14.01000 ; sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
NC 14.01000 ; sp2 N in 6 memb.ring w/LP (ADE,GUA)
N2 14.01000 ; sp2 N in amino groups
N3 14.01000 ; sp3 N for charged amino groups (Lys, etc)
N* 14.01000 ; sp2 N
NQ 14.01000 ; new amber99sb-ucb,ASN,GLN,LYN(neutral LYS) added at 09.07.2020
O 16.00000 ; carbonyl group oxygen
OR 16.00000 ; new amber99sb-ucb,TYR added at 09.07.2020
OW 16.00000 ; oxygen in TIP3P water
OH 16.00000 ; oxygen in hydroxyl group
OS 16.00000 ; ether and ester oxygen
O2 16.00000 ; carboxyl and phosphate group oxygen
P 30.97000 ; phosphate,pol:JACS,112,8543,90,K.J.Miller
S 32.06000 ; S in disulfide linkage,pol:JPC,102,2399,98
SH 32.06000 ; S in cystine
CU 63.55000 ; copper
FE 55.00000 ; iron
K 39.10000 ; potassium
Rb 85.47000 ; rubidium
Cs 132.90000 ; cesium
OW_spc 15.99940 ; SPC Water OW
HW_spc 1.00800 ; SPC Water HW
Li 6.94000 ; lithium, ions pol:J.PhysC,11,1541,(1978)
Zn 65.40000 ; Zn2+
HW_tip4pew 1.00800 ; tip4pEW HW
OW_tip4pew 16.00000 ; tip4pEW OW
HW_tip4p 1.00800 ; tip4p HW
OW_tip4p 16.00000 ; tip4p OW
HW_tip5p 1.00800 ; tip5p HW
OW_tip5p 16.00000 ; tip5p OW
MW 0.00000 ; Virtual site for tip4p/5p water point charge
MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group
MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group