H       1.00800     ; polar H
HC      1.00800     ; N-ter H
HA      1.00800     ; nonpolar H
HT      1.00800     ; TIPS3P WATER HYDROGEN
HP      1.00800     ; aromatic H
HB      1.00800     ; backbone H
HR1     1.00800     ; his he1, (+) his HG,HD2
HR2     1.00800     ; (+) his HE1
HR3     1.00800     ; neutral his HG, HD2
HS      1.00800     ; thiol hydrogen
HE1     1.00800     ; for alkene; RHC=CR
HE2     1.00800     ; for alkene; H2C=CR
HA1     1.00800     ; alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
HA2     1.00800     ; alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
HA3     1.00800     ; alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
HF1     1.00800     ; Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str)
HF2     1.00800     ; Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str)
C       12.01100    ; carbonyl C, peptide backbone
CA      12.01100    ; aromatic C
CT1     12.01100    ; aliphatic sp3 C for CH
CT2     12.01100    ; aliphatic sp3 C for CH2
CT3     12.01100    ; aliphatic sp3 C for CH3
CPH1    12.01100    ; his CG and CD2 carbons
CPH2    12.01100    ; his CE1 carbon
CPT     12.01100    ; trp C between rings
CY      12.01100    ; TRP C in pyrrole ring
CP1     12.01100    ; tetrahedral C (proline CA)
CP2     12.01100    ; tetrahedral C (proline CB/CG)
CP3     12.01100    ; tetrahedral C (proline CD)
CC      12.01100    ; carbonyl C, asn,asp,gln,glu,cter,ct2
CD      12.01100    ; carbonyl C, pres aspp,glup,ct1
CPA     12.01100    ; heme alpha-C
CPB     12.01100    ; heme beta-C
CPM     12.01100    ; heme meso-C
CM      12.01100    ; heme CO carbon
CS      12.01100    ; thiolate carbon
CE1     12.01100    ; for alkene; RHC=CR
CE2     12.01100    ; for alkene; H2C=CR
CST     12.01100    ; CO2 carbon
CT      12.01100    ; aliphatic sp3 C, new LJ params, no hydrogens (see toppar_all22_prot_aliphatic_c27.str)
CT1x    12.01100    ; aliphatic sp3 C for CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
CT2x    12.01100    ; aliphatic sp3 C for CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
CT3x    12.01100    ; aliphatic sp3 C for CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
CN      12.01100    ; C for cyano group (see toppar_all22_prot_pyridines.str)
CAP     12.01100    ; aromatic C for pyrimidines (see toppar_all22_prot_pyridines.str)
COA     12.01100    ; carbonyl C for pyrimidines (see toppar_all22_prot_pyridines.str)
C3      12.01100    ; cyclopropyl carbon
N       14.00700    ; proline N
NR1     14.00700    ; neutral his protonated ring nitrogen
NR2     14.00700    ; neutral his unprotonated ring nitrogen
NR3     14.00700    ; charged his ring nitrogen
NH1     14.00700    ; peptide nitrogen
NH2     14.00700    ; amide nitrogen
NH3     14.00700    ; ammonium nitrogen
NC2     14.00700    ; guanidinium nitroogen
NY      14.00700    ; TRP N in pyrrole ring
NP      14.00700    ; Proline ring NH2+ (N-terminal)
NPH     14.00700    ; heme pyrrole N
NC      14.00700    ; N for cyano group (see toppar_all22_prot_pyridines.str)
O       15.99900    ; carbonyl oxygen
OB      15.99900    ; carbonyl oxygen in acetic acid
OC      15.99900    ; carboxylate oxygen
OH1     15.99900    ; hydroxyl oxygen
OS      15.99940    ; ester oxygen
OT      15.99940    ; TIPS3P WATER OXYGEN
OM      15.99900    ; heme CO/O2 oxygen
OST     15.99900    ; CO2 oxygen
OCA     15.99900    ; carbonyl O for pyrimidines (see toppar_all22_prot_pyridines.str)
S       32.06000    ; sulphur
SM      32.06000    ; sulfur C-S-S-C type
SS      32.06000    ; thiolate sulfur
HE      4.00260     ; helium
NE      20.17970    ; neon
CF1     12.01100    ; monofluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
CF2     12.01100    ; difluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
CF3     12.01100    ; trifluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
FE      55.84700    ; heme iron 56
CLAL    35.45300    ; Chlorine Atom (see toppar_all22_prot_aldehydes.str)
FA      18.99800    ; aromatic flourine (see toppar_all22_prot_pyridines.str)
F1      18.99800    ; Fluorine, monofluoro (see toppar_all22_prot_fluoro_alkanes.str)
F2      18.99800    ; Fluorine, difluoro (see toppar_all22_prot_fluoro_alkanes.str)
F3      18.99800    ; Fluorine, trifluoro (see toppar_all22_prot_fluoro_alkanes.str)
DUM     0.00000     ; dummy atom
HL      1.008000    ; polar H (equivalent to protein H)
HCL     1.008000    ; charged H for PE (equivalent to protein HC)
HOL     1.008000    ; Nucleic acid phosphate hydroxyl proton
HAL1    1.008000    ; alphatic proton
HAL2    1.008000    ; alphatic proton
HAL3    1.008000    ; alphatic proton
HEL1    1.008000    ; for alkene; RHC=CR
HEL2    1.008000    ; for alkene; H2C=CR
CL      12.011000   ; carbonyl C (acetic acid/methyl acetate)
CTL1    12.011000   ; sp3 carbon with 1 H (-CH1-)
CTL2    12.011000   ; carbon of methylene group (-CH2-)
CTL3    12.011000   ; carbon of methyl group (-CH3)
CTL5    12.011000   ; carbon of methyl group (-CH3) for tetramethylammonium
CEL1    12.011000   ; for alkene; RHC=CR
CEL2    12.011000   ; for alkene; H2C=CR
NTL     14.007000   ; ammonium nitrogen
NH3L    14.007000   ; nitrogen phosphatidylethanolamine
OBL     15.999400   ; acetic acid carboxyl oxygen (e. to protein OB)
OCL     15.999400   ; acetate oxygen
OSL     15.999400   ; Nucleic acid phosphate ester oxygen
O2L     15.999400   ; Nucleic acid =O in phosphate or sulfate
OHL     15.999400   ; Nucleic acid phosphate hydroxyl oxygen
PL      30.974000   ; phosphorus
SL      32.060000   ; Sulfate sulfur
SOD     22.989770   ; Sodium Ion
MG      24.305000   ; Magnesium Ion
POT     39.102000   ; Potassium Ion! check masses
CES     132.900000  ; Cesium Ion
CAL     40.080000   ; Calcium Ion
CLA     35.450000   ; Chloride Ion
ZN      65.370000   ; zinc (II) cation
CC1A    12.01100    ; alkene conjugation
CC1B    12.01100    ; alkene conjugation
CC2     12.01100    ; alkene conjugation
NS1     14.00700    ; N for deprotonated Schiff's base
NS2     14.00700    ; N for protonated Schiff's base
OWT3    15.9994     ; TIP3P
HWT3    1.0080      ; TIP3P
OWT4    15.9994     ; TIP4P
HWT4    1.0080      ; TIP4P
MWT4    0.0000      ; TIP4P
OWT4EW  15.9994     ; TIP4PEW
HWT4EW  1.0080      ; TIP4PEW
MWT4EW  0.0000      ; TIP4PEW
OWT5    15.9994     ; TIP5P
HWT5    1.0080      ; TIP5P
MWT5    0.0000      ; TIP5P
MNH3    0.0000      ; vsite (rigid tetrahedrical NH3 group)
MNH2    0.0000      ; vsite
MCH3    0.0000      ; vsite (rigid CH3 group connected to carbons)
MCH3S   0.0000      ; vsite (rigid CH3 group connected to S)
; DNA and RNA section
P       30.974      ; Phosphorus ### For DNA
P2      30.974000   ; pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str) ### For DNA
P3      30.974000   ; protonated pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str) ### For DNA
HN1     1.008000    ; Nucleic acid amine proton ### For DNA
HN2     1.008000    ; Nucleic acid ring nitrogen proton ### For DNA
HN3     1.008000    ; Nucleic acid aromatic carbon proton ### For DNA
HN3B    1.008000    ; NAD+ aromatic hydrogen ### For DNA
HN3C    1.008000    ; Standard aromatic hydrogen (as in benzene) ### For DNA
HNP     1.008000    ; pure aromatic H ### For DNA
HN4     1.008000    ; Nucleic acid phosphate hydroxyl proton ### For DNA
HN5     1.008000    ; Nucleic acid ribose hydroxyl proton ### For DNA
HN6     1.008000    ; Nucleic acid ribose aliphatic proton ### For DNA
HN7     1.008000    ; Nucleic acid proton (equivalent to protein HA) ### For DNA
HN8     1.008000    ; Bound to CN8 in nucleic acids/model compounds ### For DNA
HN9     1.008000    ; Bound to CN9 in nucleic acids/model compounds ### For DNA
HNE1    1.008000    ; for alkene; RHC=CR (modified thy patch Sasha) ### For DNA
HNE2    1.008000    ; for alkene; H2C=CR (modified thy patch Sasha) ### For DNA
CN1     12.011000   ; Nucleic acid carbonyl carbon ### For DNA
CN1A    12.011000   ; NAD+/NADH amide carbonyl carbon ### For DNA
CN1T    12.011000   ; Nucleic acid carbonyl carbon (T/U C2) ### For DNA
CN2     12.011000   ; Nucleic acid aromatic carbon to amide ### For DNA
CN3     12.011000   ; Nucleic acid aromatic carbon ### For DNA
CN3A    12.011000   ; NAD+ aromatic carbon ### For DNA
CN3B    12.011000   ; NAD+ aromatic carbon ### For DNA
CN3C    12.011000   ; NADH aromatic carbon ### For DNA
CN3D    12.011000   ; Nucleic acid aromatic carbon for 5MC ### For DNA
CN3T    12.011000   ; Nucleic acid aromatic carbon, Thy C5 ### For DNA
CN4     12.011000   ; Nucleic acid purine C8 and ADE C2 ### For DNA
CN5     12.011000   ; Nucleic acid purine C4 and C5 ### For DNA
CN5G    12.011000   ; Nucleic acid guanine C5 ### For DNA
CN7     12.011000   ; Nucleic acid carbon (equivalent to protein CT1) ### For DNA
CN7B    12.011000   ; Nucleic acid aliphatic carbon for C1' ### For DNA
CN7C    12.011000   ; C2' in arabinose ### For DNA
CN7D    12.011000   ; C2' in nucleic acids fluorine derivatives ### For DNA
CN8     12.011000   ; Nucleic acid carbon (equivalent to protein CT2) ### For DNA
CN8B    12.011000   ; Nucleic acid carbon (equivalent to protein CT2) ### For DNA
CN9     12.011000   ; Nucleic acid carbon (equivalent to protein CT3) ### For DNA
CNE1    12.011000   ; for alkene; RHC=CR (modified thy patch Sasha) ### For DNA
CNE2    12.011000   ; for alkene; H2C=CR (modified thy patch Sasha) ### For DNA
CNA     12.011000   ; pure aromatic carbon ### For DNA
CNA2    12.011000   ; pure aromatic carbon bound to F ### For DNA
CN6     12.011000   ; carbocyclic sugar (see toppar_all27_na_carbocyclic.str) ### For DNA
CN7E    12.011000   ; carbocyclic sugar (see toppar_all27_na_carbocyclic.str) ### For DNA
NN1     14.007000   ; Nucleic acid amide nitrogen ### For DNA
NN1C    14.007000   ; Nucleic acid imino nitrogen (cyt taut Sasha) ### For DNA
NN2     14.007000   ; Nucleic acid protonated ring nitrogen ### For DNA
NN2B    14.007000   ; From NN2, for N9 in GUA different from ADE ### For DNA
NN2C    14.007000   ; Nucleic acid protonated ring nitrogen (cyt taut Sasha) ### For DNA
NN2U    14.007000   ; Nucleic acid protonated ring nitrogen, ura N3 ### For DNA
NN2G    14.007000   ; Nucleic acid protonated ring nitrogen, gua N1 ### For DNA
NN3     14.007000   ; Nucleic acid unprotonated ring nitrogen ### For DNA
NN3A    14.007000   ; Nucleic acid unprotonated ring nitrogen, ade N1 and N3 ### For DNA
NN3I    14.007000   ; Nucleic acid unprotonated ring nitrogen, inosine N3 ### For DNA
NN3G    14.007000   ; Nucleic acid unprotonated ring nitrogen, gua N3 ### For DNA
NN4     14.007000   ; Nucleic acid purine N7 ### For DNA
NN5     14.007000   ; Nucleic acid sp2 amine nitrogen ### For DNA
NN6     14.007000   ; Nucleic acid sp3 amine nitrogen (equiv to protein nh3) ### For DNA
ON1     15.999400   ; Nucleic acid carbonyl oxygen ### For DNA
ON1C    15.999400   ; Nucleic acid carbonyl oxygen, cyt O2 ### For DNA
ON2     15.999400   ; Nucleic acid phosphate ester oxygen ### For DNA
ON3     15.999400   ; Nucleic acid =O in phosphate ### For DNA
ON4     15.999400   ; Nucleic acid phosphate hydroxyl oxygen ### For DNA
ON5     15.999400   ; Nucleic acid ribose hydroxyl oxygen ### For DNA
ON6     15.999400   ; Nucleic acid deoxyribose ring oxygen ### For DNA
ON6B    15.999400   ; Nucleic acid ribose ring oxygen ### For DNA
ON2B    15.999400   ; Nucleic acid phosphate ester oxygen (pres tp1/tp2, toppar_tyr_ser_thr_phosphate.str) ### For DNA
FN1     18.998400   ; Fluorine for sugar derivatives (NF) ### For DNA
FNA     18.998400   ; Aromatic fluorine ### For DNA
CC1A    12.011000   ; alkene conjugation ### For DNA
CC1B    12.011000   ; alkene conjugation ### For DNA
CC2     12.011000   ; alkene conjugation ### For DNA
NS1     14.007000   ; N for deprotonated Schiff's base ### For DNA
NS2     14.007000   ; N for protonated Schiff's base ### For DNA
SP      32.060000   ; positive Sulphur, S-adenosylmethionine (SAM) ### For DNA
CPH1    12.011000   ; For imidazole model compound (NF)
CPH2    12.011000   ; For imidazole model compound (NF)
HR3     1.008000    ; For imidazole model compound (NF)
HR1     1.008000    ; For imidazole model compound (NF)
NR1     14.007000   ; For nitrogen in imidazol (NF)
NR2     14.007000   ; For nitrogen in imidazol (NF)
DUM_OH1   15.999400
DUM_H     1.008000
DUM_HA    1.008000
DUM_S    32.060000
DUM_HS    1.008000
DUM_OB   15.999400
DUM_OC   15.999400
DUM_CC   12.011000
DUM_CA   12.011000
DUM_HP    1.008000
DUM_CPH1   12.011000
DUM_NR1   14.007000
DUM_HR3    1.008000
DUM_CPH2   12.011000
DUM_HR1    1.008000
DUM_NR2   14.007000
DUM_CT3   12.011000
DUM_CD   12.011000
DUM_CT2   12.011000
DUM_NH3   14.007000
DUM_HC    1.008000
DUM_O    15.999400
DUM_NH2   14.007000
DUM_NC2   14.007000
DUM_C    12.011000
DUM_CPT   12.011000
DUM_NY   14.007000
DUM_NR3   14.007000
DUM_HR2    1.008000
DUM_CT1   12.011000
DUM_CY   12.011000
DUM_NH1   14.007000
DUM_HB    1.008000
DUM_N    14.007000
DUM_CP1   12.011000
DUM_CP2   12.011000
DUM_CP3   12.011000
