Atom types (GROMOS 54A7)ΒΆ
Defined atom types in the GROMOS 54A7 force field.
Type |
Mass |
Description |
|---|---|---|
O |
15.99940 |
carbonyl oxygen (C=O) |
OM |
15.99940 |
carboxyl oxygen (CO-) |
OA |
15.99940 |
hydroxyl, sugar or ester oxygen |
OE |
15.99940 |
ether or ester oxygen |
OW |
15.99940 |
water oxygen |
N |
14.00670 |
peptide nitrogen (N or NH) |
NT |
14.00670 |
terminal nitrogen (NH2) |
NL |
14.00670 |
terminal nitrogen (NH3) |
NR |
14.00670 |
aromatic nitrogen |
NZ |
14.00670 |
Arg NH (NH2) |
NE |
14.00670 |
Arg NE (NH) |
C |
12.01100 |
bare carbon |
CH0 |
12.0110 |
bare sp3 carbon, 4 bound heavy atoms |
CH1 |
13.01900 |
aliphatic or sugar CH-group |
CH2 |
14.02700 |
aliphatic or sugar CH2-group |
CH3 |
15.03500 |
aliphatic CH3-group |
CH4 |
16.04300 |
methane |
CH2r |
14.02700 |
CH2-group in a ring |
CR1 |
13.01900 |
aromatic CH-group |
HC |
1.00800 |
hydrogen bound to carbon |
H |
1.00800 |
hydrogen not bound to carbon |
DUM |
0.00000 |
dummy atom, no idea what the mass should be. PT3-99 |
S |
32.06000 |
sulfur |
CU1+ |
63.54600 |
copper (charge 1+) |
CU2+ |
63.54600 |
copper (charge 2+) |
FE |
55.84700 |
iron (heme) |
ZN2+ |
65.37000 |
zinc (charge 2+) |
MG2+ |
24.30500 |
magnesium (charge 2+) |
CA2+ |
40.08000 |
calcium (charge 2+) |
P |
30.97380 |
phosphor |
AR |
39.94800 |
argon |
F |
18.99840 |
fluor (non-ionic) |
CL |
35.45300 |
chlorine (non-ionic) |
BR |
79.90400 |
bromine (non-ionic) |
CMET |
15.035 |
CH3-group in methanol (solvent) |
OMET |
15.9994 |
oxygen in methanol (solvent) |
NA+ |
22.9898 |
sodium (charge 1+) |
CL- |
35.45300 |
chlorine (charge 1-) |
CCHL |
12.011 |
carbon in chloroform (solvent) |
CLCHL |
35.453 |
chloride in chloroform (solvent) |
HCHL |
1.008 |
hydrogen in chloroform (solvent) |
SDMSO |
32.06000 |
DMSO Sulphur (solvent) |
CDMSO |
15.03500 |
DMSO Carbon (solvent) |
ODMSO |
15.99940 |
DMSO Oxygen (solvent) |
CCL4 |
12.011 |
carbon in carbontetrachloride (solvent) |
CLCL4 |
35.453 |
chloride in carbontetrachloride (solvent) |
FTFE |
18.99840 |
fluor in trifluoroethanol |
CTFE |
12.01100 |
carbon in trifluoroethanol |
CHTFE |
14.0270 |
CH2-group in trifluoroethanol |
OTFE |
15.99940 |
oxygen in trifluoroethanol |
CUREA |
12.01100 |
carbon in urea |
OUREA |
15.99940 |
oxygen in urea |
NUREA |
14.00670 |
nitrogen in urea |
SI |
28.08 |
silicon |
MNH3 |
0 |
Dummy mass in rigid tetraedrical NH3 group |
MW |
0 |
Dummy mass in rigid tyrosine rings |
CH3p |
15.03500 |
Polar aliphatic CH3-group |