Download Force field parameters Tables 2.4.1 Mass atom type codes, masses

Force field parameters
54A7
Tables
2.4.1
2.5.2.1
2.5.3.1
2.5.4.1
2.5.5.1.1
2.5.6.2.1
2.5.6.2.2
2.5.6.2.3
2.5.6.2.4
2.5.6.2.5
2.5.6.3.1
2.5.6.5.1
2.5.6.5.2
2.5.6.5.3
2.5.6.5.4
2.5.6.5.5
4.2.1
4.2.2
4.2.3
Mass atom type codes, masses and names
Bond stretching parameters
Bond-angle bending parameters
Improper (harmonic) dihedral angle parameters
(Trigonometric) dihedral torsional angle parameters
Non-bonded atom types and integer atom codes
Normal van der Waals parameters
(Vacuo) normal van der Waals parameters
Selection of van der Waals (repulsive) C12½ (I,I) parameters
Normal van der Waals parameters for mixed atom type pairs (I,J)
Third-neighbour van der Waals parameters
Atomic charges and charge group definitions for amino acid residues
Atomic charges for various (co)solvents
Atomic charges and charge group definitions for nucleotides
Atomic charges and charge group definitions for lipids
Atomic charges and charge group definitions for carbohydrates
54A7 Solute building blocks
54A7 Solvent building blocks
54A7 End group building blocks
Changes with respect to 53A6 in bold

Torsional angle energy terms for the polypeptide  and  dihedral
angles are changed

The choice of the C12 parameter for the interaction between O(IAC=1)
and N(IAC=6)

A new van der Waals nonbonded atom type for a charged CH3 group
is added (IAC=54)

The van der Waals parameters for the Na+(IAC=37) and CL-(IAC=38)
are modified [A578]

Two extra improper dihedral angle terms have been added to facilitate
free energy calculations
1
Table 2.4.1
GROMOS mass atom type codes, masses and names
mass atom type code
N
1
3
4
5
6
12
14
16
19
23
24
28
31
32
35
39
40
56
63
65
80
mass in a.m.u.
ATMAS[N]
1.008
13.019
14.027
15.035
16.043
12.011
14.0067
15.9994
18.9984
22.9898
24.305
28.08
30.9738
32.06
35.453
39.948
40.08
55.847
63.546
65.37
79.904
mass atom name
ATMASN[N]
H
CH1
CH2
CH3
CH4
C
N
O
F
NA
MG
SI
P
S
CL
AR
CA
FE
CU
ZN
BR
2
Table 2.5.2.1
GROMOS bond-stretching parameters
Bond-type code
Force constant
Ideal bond length
K bn
b0n
K bharm
n
nm
B0[N]
kcalmol-1Å-2
harm
= K bn
ICBH[N]
ICB[N]
1
2
3
4
5
6
7
8
9
10
Examples of usage in
terms of nonbonded atom
types
/ 2b02n
106kJmol-1nm-4
CB[N]
15.7
18.7
12.3
37.0
16.6
13.4
12.0
8.87
10.6
11.8
0.100
0.100
0.109
0.112
0.123
0.125
0.132
0.133
0.133
0.133
11
12
13
14
15
16
10.5
11.7
10.2
11.0
8.66
10.8
0.134
0.134
0.136
0.138
0.139
0.139
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
8.54
8.18
9.21
6.10
8.71
5.73
7.64
8.60
8.37
5.43
7.15
4.84
4.72
2.72
5.94
5.62
3.59
0.140
0.143
0.143
0.1435
0.147
0.148
0.148
0.148
0.150
0.152
0.153
0.161
0.163
0.178
0.178
0.183
0.187
3
H – OA
H – N (all)
HC – C
C – O (CO bound to heme)
C –O
C – OM
CR1 – NR (6-ring)
H – S
C – NT, NL
C, CR1 – N, NR, CR1, C
(peptide, 5-ring)
C – N, NZ, NE
C – NR (no H) (6-ring)
C – OA, FTfe – CTfe
C – NR (heme)
CH2 – C, CR1 (6-ring)
C, CR1 – CH2, C, CR1
(6–ring)
C, CR1, CH2 – NR (6-ring)
CHn – OA
CHn – OM
CHn – OA (sugar)
CHn – N, NT, NL, NZ, NE
CHn – NR (5-ring)
CHn – NR (6-ring)
O, OM – P
O – S
CHn – CHn (sugar)
C, CHn – C, CHn
OA – P
OA – SI
FE – C (CO bound to heme)
CH3 – S
CH2 – S
CH1 – SI
750
895
700
2220
1200
1000
1000
750
900
1000
900
1000
900
1000
800
1000
800
800
900
600
900
600
800
900
900
600
800
600
600
412
900
900
600
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
0.640
0.628
5.03
0.540
23.2
12.1
8.12
8.04
4.95
8.10
13.1
10.3
8.71
2.68
2.98
2.39
2.19
3.97
3.04
0.198
0.200
0.204
0.221
0.100
0.110
0.1758
0.153
0.193799
0.176
0.1265
0.135
0.163299
0.233839
0.290283
0.279388
0.291189
0.2077
0.287407
4
NR (His) – FE (43A1)
NR (heme) – FE
S – S
NR (His) – FE
HWat – OWat
HChl – CChl
CChl – CLChl
ODmso – SDmso
SDmso – CDmso
CCl4 – CLCl4
CUrea – OUrea
CUrea – NUrea
HWat – HWat
HChl – CLChl
CLChl – CLChl
ODmso – CDmso
CDmso – CDmso
HMet – CMet
CLCl4 – CLCl4
120
120
1000
126
1110
700
1200
900
890
1200
1000
900
1110
700
1200
890
890
820
1200
Table 2.5.3.1
GROMOS bond-angle bending parameters
Bond-angle type
code
Force constant
Ideal bond
angle
0
Kn
 g ( K
harm
ICTH[N]
ICT[N]
1
n
Example of usage in terms of
nonbonded atom types
Kharm
n
n
,  n , Ek T )
kJmol-1
CT[N]
0
B
kcalmol-1rad-2
degree
(T0[N])
380
90.0
2
420
90.0
3
4
5
6
7
8
405
475
420
490
465
285
96.0
100.0
103.0
104.0
108.0
109.5
9
320
109.5
10
380
109.5
11
425
109.5
12
13
450
520
109.5
109.5
14
15
450
530
109.6
111.0
16
17
18
19
20
21
22
23
24
25
545
50.0
460
610
465
620
635
390
445
505
113.0
115.0
115.0
115.0
116.0
116.0
117.0
120.0
120.0
120.0
26
27
28
530
560
670
120.0
120.0
120.0
5
NR (heme) – FE – C (CO bound to
heme)
NR(heme) – FE – NR(heme), NR
(His)
H – S – CH2
CH2 – S – CH3
OA – P – OA
CH2 – S – S
NR, C, CR1(5–ring)
CHn – CHn – CHn, NR(6-ring)
(sugar)
CHn, OA – CHn – OA, NR(ring)
(sugar)
H – NL, NT – H, CHn – OA –
CHn(sugar)
H – NL – C, CHn
H – NT –
CHn
X – OA, SI – X
CH ,C – CHn – C, CHn, OA,OM,
N, NE
OM – P – OA
CHn – CHn – C, CHn, OA, NR,
NT, NL
CHn – CH2 – S
NR(heme) – FE – NR (His) (43A1)
H – N – CHn
CHn, C – C – OA, N, NT, NL
H – NE – CH2
CH2 – N – CH1
CH3 – N – C, CHn – C – OM
H – NT, NZ, NE – C
H – NT, NZ – H
H – N – CH3, H, HC – 6-ring, H –NT
– CHn
P, SI – OA – CHn, P
N, C, CR1 (6-ring, no H)
NZ – C – NZ, NE
90
100
95
110
95
110
100
60
68
80
90
95
110
95
110
110
10
90
120
90
120
120
70
80
90
95
100
120
29
30
780
685
120.0
121.0
31
32
33
700
415
730
122.0
123.0
124.0
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
375
750
575
640
770
760
2215
91350
434
484
632
469
503
443
618
507
448
524
531
636
690
125.0
125.0
126.0
126.0
126.0
132.0
155.0
180.0
109.5
107.57
111.30
97.4
106.75
108.53
109.5
107.6
109.5
110.3
111.4
117.2
121.4
6
OM – P – OM
O – C – CHn, C
CH3 – N –
CHn
CH1, CH2 – N – C
H –N –C
O – C – OA, N, NT, NL C – NE –
CH2
FE – NR – CR1 (5-ring)
–
H, HC – 5-ring
X(noH) – 5-ring
OM – C – OM
5, 6 ring connnection
SI – OA – SI
Fe – C – O (CO bound to heme)
HWat – OWat – HWat
HChl – CChl – CLChl
CLChl – CChl – CLChl
CDmso – SDmso – CDmso
CDmso – SDmso – ODmso
HMet – OMet – CMet
CLCl4 – CCl4 – CLCl4
FTfe – CTfe – FTfe
HTfe – OTfe – CHTfe
OTfe – CHTfe – CTfe
CHTfe – CTfe – FTfe
NUrea – CUrea – NUrea
OUrea – CUrea – NUrea
140
120
120
70
120
60
120
90
100
120
100
95
57
92
105
131
110
110
95
131
110
95
110
110
120
120
Table 2.5.4.1
GROMOS improper (harmonic) dihedral angle parameters
Improper
dihedral-angle
type code
ICQH[N]
ICQ[N]
1
2
3
4
5
Force constant
Ideal improper
dihedral angle
K n
0
kJmol-1 degree-2
CQ[N]
degree
(Q0[N])
Example of usage
K n
n
kcalmol-1 rad-2
0.0510
0.102
0.0
35.26439
0.204
0.0510
0.102
0.0
180.0
-35.26439
7
planar groups
tetrahedral
centres
heme iron
planar groups
tetrahedral
centres
40
80
160
40
80
Table 2.5.5.1
GROMOS (trigonometric) dihedral torsional angle parameters
Dihedralangle type
code
ICPH[N]
ICP[N]
1
Force
constant
Phase shift
Multiplici
ty
Kn
cos(δn)
mn
kJmol-1
CP[N]
Example of usage in
terms of nonbonded
atom types
K n
kcalmol-1
PD[N]
NP[N]
2.67
-1.0
1
2
3.41
-1.0
1
3
4.97
-1.0
1
4
5.86
-1.0
1
5
9.35
-1.0
1
6
9.45
-1.0
1
7
8
9
2.79
5.35
1.53
+1.0
+1.0
-1.0
1
1
2
10
11
12
13
5.86
7.11
16.7
24.0
-1.0
-1.0
-1.0
-1.0
2
2
2
2
14
15
16
17
18
19
20
33.5
41.8
0.0
0.418
2.09
3.14
5.09
-1.0
-1.0
+1.0
+1.0
+1.0
+1.0
+1.0
2
2
2
2
2
2
2
21
22
23
24
16.7
1.05
1.26
1.30
+1.0
+1.0
+1.0
+1.0
2
3
3
3
25
2.53
+1.0
3
CHn – CHn – CHn – OA
(sugar)
C4 – C5 – C6 – O6 a
OA – CHn – OA – CHn, H
( sugar)
O5 – C1 – O1 – C1’,H1
OA – CHn – CHn – OA
(sugar)
C4 – C5 – C6 – O6 a
N – CHn – CHn – OA
(lipid)
OA – CHn – CHn – OA
(sugar)
O5 – C5 – C6 – O6 b
OA – CHn – OA – CHn, H
( sugar)
O5 – C1 – O1 – C1’,H1
P – O5* – C5* – C4* (dna)
O5* – C5* – C4* – O4* (dna)
C1 – C2 – CAB – CBB
(heme)
–C–C–
–C–OA– (at ring)
–C–OA– (carboxyl)
CHn – OA – C – CHn (ester
lipid)
–C–N, NT, NE, NZ,NR–
–C–CR1– (6-ring)
–CH1 (sugar)–NR(base)–
O–CH1–CHn–no O
O–CH1–CHn–O
–OA–P–
CHn – O – P – O (dna,
phosphodiester)
–S–S–
–OA–P–
–CHn–OA(no sugar)–
HTfe – OTfe – CHTfe –
CTfe
O5* – C5* – C4* – O4* (dna)
8
0.6
0.8
1.2
1.4
2.2
2.3
0.7
1.3
0.4
1.4
1.7
4.0
5.7
8.0
10.0
0.0
0.1
0.5
0.75
1.2
4.0
0.25
0.3
0.3
0.6
26
27
2.93
3.19
+1.0
+1.0
3
3
28
3.65
+1.0
3
29
3.77
+1.0
3
30
3.90
+1.0
3
31
32
4.18
4.69
+1.0
+1.0
3
3
33
34
35
5.44
5.92
7.69
+1.0
+1.0
+1.0
3
3
3
36
8.62
+1.0
3
37
9.50
+1.0
3
38
39
40
41
42
43
44
45
0.0
1.0
1.0
3.77
3.50
2.80
0.70
0.40
+1.0
-1.0
+1.0
+1.0
-1.0
+1.0
-1.0
+1.0
4
6
6
6
2
3
6
6
–CH2–S–
CHn – O – P – O (dna,
phosphodiester)
OA – CHn – OA – CHn, H
( sugar)
O5 – C1 – O1 – C1’,H1
–C,CHn,SI–
NT,NL,OA(sugar)–
CHn – CHn – OA – H
(sugar)
HC–C–S–
OA – CHn – OA – CHn, H
( sugar)
O5 – C1 – O1 – C1’,H1
HC–C–C–
–CHn,SI–CHn–
OA – CHn – CHn – OA
(sugar)
C4 – C5 – C6 – O6 a
N – CHn – CHn – OA
(lipid)
OA – CHn – CHn – OA
(sugar)
O5 – C5 – C6 – O6 b
–NR–FE–
–CHn–N,NE–
–CHn–C,NR (ring), CR1–
–CHn–NT–
–CHn–C–
–CHn–N–
–CHn–N–
–CHn–C–
0.7
0.8
0.9
0.9
0.9
1.0
1.1
1.3
1.4
1.8
2.1
2.3
0.0
0.24
0.24
0.9
0.84
0.67
0.17
0.10
a) To be used if – C5 – C6 – O6 and adjacent – C4 – O4 – are axial and the other equatorial, as in galactose
b) To be used if – C5 – C6 – O6 and adjacent – Cn – On – Hn are both simultaneously axial or equatorial, as in
glucose
9
Table 2.5.6.2.1
GROMOS 54A7/54B7 non-bonded atom types and integer atom codes
integer atom code
IAC[N]
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
atom type
TYPE[N]
O
OM
OA
OE
OW
N
NT
NL
NR
NZ
NE
C
CH0
CH1
CH2
CH3
CH4
CH2r
CR1
HC
H
DUM
S
CU1+
CU2+
FE
ZN2+
MG2+
CA2+
P, SI
AR
F
CL
BR
CMet
OMet
NA+
CLCChl
CLChl
HChl
SDmso
description
carbonyl oxygen (C=O)
carboxyl oxygen (CO-)
hydroxyl or sugar oxygen
ether or ester oxygen
water oxygen
peptide nitrogen (NH)
terminal nitrogen (NH2)
terminal nitrogen (NH3)
aromatic nitrogen
Arg NH (NH2)
Arg NE (NH)
bare carbon
bare sp3 carbon, 4 bound heavy atoms
aliphatic or sugar CH-group
aliphatic or sugar CH2-group
aliphatic CH3-group
methane
CH2-group in a ring
aromatic CH-group
hydrogen bound to carbon
hydrogen not bound to carbon
dummy atom
sulphur
copper (charge 1+)
copper (charge 2+)
iron (heme)
zinc (charge 2+)
magnesium (charge 2+)
calcium (charge 2+)
phosphor or silicon
argon
fluor (non-ionic)
chlorine (non-ionic)
bromine (non-ionic)
CH3-group in methanol (solvent)
oxygen in methanol (solvent)
sodium (charge 1+)
chloride (charge 1-)
carbon in chloroform (solvent)
chloride in chloroform (solvent)
hydrogen in chloroform (solvent)
sulphur in DMSO (solvent)
10
43
44
45
46
47
48
49
50
51
52
53
54
CDmso
ODmso
CCl4
CLCl4
FTfe
CTfe
CHTfe
OTfe
CUrea
OUrea
NUrea
CH3p
CH3-group in DMSO (solvent)
oxygen in DMSO (solvent)
carbon in carbontetrachloride (solvent)
chloride in carbontetrachloride (solvent)
fluor in trifluoroethanol
carbon in trifluoroethanol
CH2-group in trifluoroethanol
oxygen in trifluoroethanol
carbon in urea
oxygen in urea
nitrogen in urea
positively charged methyl
11
Table 2.5.6.2.2
GROMOS 54A7 normal van der Waals parameters
integer atom
code
atom type
(C12(I,I))½
(C6(I,I))½
[kJmol-1 nm6]½
I=IAC[N]
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
TYPE[N]
O
OM
OA
OE
OW
N
NT
NL
NR
NZ
NE
C
CH0
CH1
CH2
CH3
CH4
CH2r
CR1
HC
H
DUM
S
CU1+
CU2+
FE
ZN2+
MG2+
CA2+
P, SI
AR
F
CL
BR
CMet
OMet
NA+
CL-
0.04756
0.04756
0.04756
0.04756
0.05116
0.04936
0.04936
0.04936
0.04936
0.04936
0.04936
0.04838
0.04896
0.07790
0.08642
0.09805
0.1148
0.08564
0.07425
0.009200
0.0
0.0
0.09992
0.02045
0.02045
0.0
0.02045
0.008080
0.03170
0.1214
0.07915
0.03432
0.09362
0.16630
0.09421
0.04756
0.0088792
0.11318
10-3[kJmol-1 nm12]½
1
1.000
0.8611
1.100
1.100
1.623
1.523
1.523
1.523
1.523
1.523
1.523
2.222
14.33
9.850
5.828
5.162
5.862
5.297
3.888
0.1230
0.0
0.0
3.616
0.07159
0.07159
0.0
0.09716
0.05838
0.7057
4.711
3.138
0.8722
3.911
8.092
4.400
1.525
0.2700
7.776
12
2
1.130
1.841
1.227
1.227
1.623
1.943
2.250
3.068
1.841
2.148
1.984
0.2250
0.4091
0.0
0.09716
0.05838
0.7057
4.711
1.227
1.525
0.2700
7.776
3
3.068
7.776
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
CChl
CLChl
HChl
SDmso
CDmso
ODmso
CCl4
CLCl4
FTfe
CTfe
CHTfe
OTfe
CUrea
OUrea
NUrea
CH3p
0.051292
0.091141
0.0061400
0.10277
0.098050
0.047652
0.051292
0.087201
0.034320
0.048380
0.084290
0.047560
0.069906
0.048620
0.057903
0.09805
2.0160
3.7101
0.065574
4.6366
5.1620
0.86686
2.7568
3.5732
1.0000
1.8370
5.0770
1.2270
3.6864
1.2609
1.9877
5.162
13
1.1250
1.0000
1.2270
1.2609
1.9877
-
-
Table 2.5.6.2.3
GROMOS 53B6 (vacuo) normal van der Waals parameters
integer atom code
atom type
(C12(I,I))½
(C6(I,I))½
[kJmol-1nm6]½
I=IAC[N]
2
8
TYPE[N]
OM
NL
0.04756 (23.25)
0.04936 (24.13)
10-3[kJmol-1nm12]½
1
0.8611 (421.0)
1.301 (636.0)
14
2
1.125 (550.0)
1.943 (950.0)
3
1.125 (550.0)
-
Table 2.5.6.2.4
Selection of van der Waals (repulsive) (C12(I,I))½ parameters
J
I
1
O
2
OM
3
OA
4
OE
5
OW
6
N
7
NT
8
NL
9
NR
10
NZ
11
NE
24
CU1+
25
CU2+
26
FE
27
ZN2+
28
MG2+
29
CA2+
30
P,SI
32
F
33
34
CL
36
OMet
37
NA+
BR
38
CL-
44
47
ODmso
50
52
53
54
OTfe
FTfe
OUrea
NUrea
CH3p
1
2
3
4
5
6
7
8
9
10
11
24
25
26
27
28
29
30
32
33
34
36
37
38
44
47
50
52
53
54
O
OM
OA
OE
OW
N
NT
NL
NR
NZ
NE
CU1+
CU2+
FE
ZN2+
MG2+
CA2+
P,SI
F
CL
BR
OMet
NA+
CL-
ODmso
FTfe
OTfe
OUrea
NUrea
CH3p
1
1
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
2
2
1
1
1
1
1
2
1
1
1
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
2
2
1
1
1
1
1
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
1
2
1
1
2
2
2
2
2
2
2
2
1
1
1
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
2
2
1
1
1
1
1
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
1
2
1
1
2
2
2
2
2
2
2
2
1
1
2
2
2
2
1
2
1
2
1
1
1
1
1
1
1
1
1
2
1
1
2
1
2
2
2
1
2
2
1
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
1
1
1
2
1
1
2
1
2
2
2
2
2
2
1
2
3
2
2
2
1
2
1
2
1
1
1
1
1
1
1
1
1
2
1
1
2
1
3
2
2
1
2
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
1
2
1
1
2
2
2
2
2
2
2
2
1
2
3
2
2
2
1
2
1
2
1
1
1
1
1
1
1
1
1
2
1
1
2
1
3
2
2
1
2
2
1
2
3
2
2
2
1
2
1
2
1
1
1
1
1
1
1
1
1
2
1
1
2
1
3
2
2
1
2
2
1
2
3
2
2
2
1
1
1
2
1
1
1
1
1
1
1
1
1
2
1
1
2
1
3
2
2
1
2
1
1
2
3
2
2
2
1
1
1
2
1
1
1
1
1
1
1
1
1
2
1
1
2
1
3
2
2
1
2
1
1
2
3
2
2
2
1
1
1
2
1
1
1
1
1
1
1
1
1
2
1
1
2
1
3
2
2
1
2
1
1
2
3
2
2
2
1
1
1
2
1
1
1
1
1
1
1
1
1
2
1
1
2
1
3
2
2
1
2
1
1
2
3
2
2
2
1
1
1
2
1
1
1
1
1
1
1
1
1
2
1
1
2
1
3
2
2
1
2
1
1
2
3
2
2
2
1
1
1
2
1
1
1
1
1
1
1
1
1
2
1
1
2
1
3
2
2
1
2
1
1
2
3
2
2
2
1
1
1
2
1
1
1
1
1
1
1
1
1
2
1
1
2
1
3
2
2
1
2
1
1
1
1
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
2
2
1
1
1
1
1
2
1
1
1
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
2
2
1
1
1
1
1
2
1
1
1
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
2
2
1
1
1
1
1
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
1
2
1
1
2
2
2
2
2
2
2
2
1
2
3
2
2
2
1
1
1
2
1
1
1
1
1
1
1
1
1
2
1
1
2
1
3
2
2
1
2
1
1
1
1
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
2
2
1
1
1
1
1
2
1
1
1
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
2
2
1
1
1
2
1
2
1
1
1
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
2
2
1
1
1
1
1
2
1
1
1
2
1
2
1
2
1
2
1
1
1
1
1
1
1
1
1
1
1
1
2
1
1
2
1
2
2
2
1
1
1
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
2
2
1
1
1
2
1
2
1
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
1
1
1
2
1
1
2
1
2
2
2
2
2
2
1
1
3
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
15
Table 2.5.6.2.5
GROMOS 54A7 normal van der Waals parameters for mixed atom type pairs (I,J)
integer atom
code
I
atom type
39
39
40
CChl
CChl
CLChl
integer atom
code
J
atom type
C6(I,J)
C12(I,J)
10-6kJmol-1nm12
40
41
41
CLChl
HChl
HChl
10-3kJmol1nm6
4.6754
0.3622
0.6493
16
7.4813
0.1745
0.3266
Table 2.5.6.3.1
GROMOS 54A7/54B7 third-neighbour van der Waals parameters
integer atom code
atom type
(C12(I,I))½
(C6(I,I))½
[kJmol-1nm6]½
I=IAC[N]
1
3
4
6
7
8
9
10
11
12
13
14
15
16
18
19
54
TYPE[N]
O
OA
OE
N
NT
NL
NR
NZ
NE
C
CH0
CH1
CH2
CH3
CH2r
CR1
CH3p
10-3[kJmol-1nm12]½
1
0.8611
1.125
1.125
1.301
1.301
1.301
1.301
1.301
1.301
1.837
1.837
1.933
2.178
2.456
2.178
2.886
2.456
0.04756
0.04756
0.04756
0.04936
0.04936
0.04936
0.04936
0.04936
0.04936
0.04838
0.04838
0.05396
0.06873
0.08278
0.06873
0.07435
0.08278
17
2
-
3
-
Table 2.5.6.5.1
GROMOS 54A7 (54B7) atomic charges and charge group definitions for amino acid residues
atom name
N
H
C
O
CD
NE
HE
CZ
NH1/2
HH11/12/21/22
NE
HE
CZ
NH1
HH1
NH2
HH21/22
CG, CD
OD1, OE1
ND2, NE2, NZ
HD21/22, HE21/22, HZ1/2
CG, CD
OD1/2, OE1/2
CG, CD
OD1, OE1
OD2, OE2
HD2, HE2
CB
SG
CB
SG
HG
CG
ND1
HD1
CD2
HD2
CE1
HE1
NE2
CG
ND1
CD2
charge in e
-0.310
0.310
0.450
-0.450
0.090 (0.0)
-0.110 (-0.240)
0.240 (0.240)
0.340 (0.0)
-0.260 (-0.480)
0.240 (0.240)
-0.310
0.310
0.266
-0.674
0.408
-0.880
0.440
0.290
-0.450
-0.720
0.440
0.270 (0.720)
-0.635 (-0.360)
0.330
-0.450
-0.288
0.408
-0.100 (0.200)
-0.400 (-0.200)
0.150
-0.370
0.220
0.0
-0.050
0.310
0.0
0.140
0.0
0.140
-0.540
0.0
-0.540
0.0
18
occurring in
all residues
all residues
Arg (charge +1)
Argn (neutral)
Argn (neutral)
Argn (neutral)
Asn, Gln
Asn, Gln
Asp, Glu (charge -1)
Asph, Gluh
Cys (charge -.5)
Cysh
Hisa (proton at D1)
Hisb (proton at E2)
HD2
CE1
HE1
NE2
HE2
CG
ND1
HD1
CD2
HD2
CE1
HE1
NE2
HE2
CG, CB, CB
OD1, OG, OG1
HD1, HG, HG1
CE
NZ
HZ1/2/3
CE
NZ
HZ1/2
CG /CE
SD
CG
CD1
HD1
CD2
NE1
HE1
CE2
CZ
OH
HH
C
0.140
0.0
0.140
-0.050
0.310
-0.050 (0.0)
0.380 (-0.300)
0.300 (0.300)
-0.100 (.0)
0.100
-0.340 (0.0)
0.100
0.310 (-0.300)
0.300 (0.300)
0.266
-0.674
0.408
0.127 (0.0)
0.129 (-0.744)
0.248 (0.248)
-0.220
-0.660
0.440
0.241
-0.482
-0.210
-0.140
0.140
0.0
-0.100
0.310
0.0
0.203
-0.611
0.408
-0.140
H
C
0.140
0.0
CH2
0.0
Hish (charge +1)
Hyp, Ser, Thr
Lysh (charge +1)
Lys (neutral)
Met
Trp
Tyr
all aromatic C-H groups in
Phe, Tyr, Trp
aromatic C connected to an
aliphatic CHn in Phe, Tyr
aliphatic CHn connected to
aromatic C in Phe, Tyr
The charges for the 53B6 force field are given between parentheses. The atoms that are not listed have
zero partial charge and form single atom or multiple atom charge groups.
19
Table 2.5.6.2
GROMOS 54A7 atomic charges for various (co)solvents
atom name
OW
HW1/2
charge in e
-0.82000
0.41000
occurring in
H2O (SPC model)
OW
HW1/2
-0.84760
0.42380
H2O (SPC/E model)
OW
HW1/2
-0.68850
0.34425
H2O (SPC/L model)
CChl
CLChl
HChl
0.17900
-0.08700
0.08200
Chloroform
SDmso
CDmso
ODmso
0.12753
0.16000
-0.44753
DMSO
CMet
OMet
HMet
0.26600
-0.67400
0.40800
Methanol
CCl4
CLCl4
0.0
0.0
Carbontetrachloride
FTFE
CTFE
CHTFE
OTFE
HTFE
-0.17000
0.45200
0.27300
-0.62500
0.41000
2,2,2-Trifluoroethanol
CUrea
OUrea
NUrea
HUrea
0.14200
-0.39000
-0.54200
0.33300
Urea
20
Table 2.5.6.5.3
GROMOS 54A7 (54B7) atomic charges and charge group definitions for nucleotides
atom name
O3/5*
P
O1/2P
C4*
O4*
C1*
N9, N9, N1, N1, N1
C4, C4
C6, C6, C6
H6, H6, H6
N1, N3, N7, N3, N7, N3
C2, C8, C8
H2, H8, H8
C6, C2, C4
N6, N2, N4
H61/62, H21/22, H41/42
N1, N3, N3
H1, H3, H3
C6, C2, C2, C4, C2, C4
O6, O2, O2, O4, O2, O4
C5, C5
H5, H5
charge in e
-0.360 (-0.360)
0.990 (1.440)
-0.635 (-0.360)
0.160
-0.360
0.200
-0.200
0.200
0.100
0.100
-0.540
0.440
0.100
0.540
-0.830
0.415
-0.310
0.310
0.450
-0.450
-0.100
0.100
21
occurring in
all nucleotides
all nucleotides
dAde, dGua, dCyt, dThy, Ura
dAde, dGua
dCyt, dThy, Ura
dCyt, dThy, Ura
dAde, dAde, dAde, dGua, dGua,
dGua, dCyt
dAde, dAde, dGua
dAde, dAde, dGua
dAde, dGua, dCyt
dAde, dGua, dCyt
dAde, dGua, dCyt
dGua, dThy, Ura
dGua, dThy, Ura
dGua, dCyt, dThy, dThy, Ura, Ura
dGua, dCyt, dThy, dThy, Ura, Ura
dCyt, Ura
dCyt, Ura
Table 2.5.6.5.4
GROMOS 54A7 (54B7) atomic charges and charge group definitions for lipids
atom name
C32, C33, C34, C35
N
C31
O31, O32
O33, O34
P
C3
C1, C2
O11, O21
O12, O22
C11, C21
C12, …, C22, …
charge in e
0.250
0.0
0.0
-0.360
-0.635
0.990
0.0
0.160
-0.360
-0.380
0.580
0.0
occurring in
dppc
dppc
dppc
dppc
dppc
dppc
dppc
dppc
dppc
dppc
dppc
dppc
22
Table 2.5.6.5.5
GROMOS 54A7 (54B7) atomic charges and charge group definitions for carbohydrates
atom name
C1, C2, C3, C6
O2, O3, O6
HO2, HO3, HO6
C5
O5
O1
C4
C6
O61, O62
C1
O1
CM (methyl)
charge in e
0.232
occurring in
glucopyranose, polyuronate,
terminal – CHn – On – Hn group
glucopyranose, polyuronate,
terminal – CHn – On – Hn group
glucopyranose, polyuronate,
terminal – CHn – On – Hn group
glucopyranose, polyuronate
glucopyranose, polyuronate
glucopyranose, polyuronate
glucopyranose, polyoronate
polyuronate
polyuronate
terminal – C1 – O1 – CM group
terminal – C1 – O1 – CM group
terminal – C1 – O1 – CM group
-0.642
0.410
0.376
-0.480
-0.360
0.232
0.360
-0.680
0.232
-0.360
0.232
23
Table 4.2.1
54A7 Solute building blocks
Name
Description (charges in e)
amino acids and analogues (L if not indicated otherwise)
ALA
Alanine
ARG
Arginine (protonated; charge +1)
ARGN
Arginine (deprotonated; neutral)
ASN
Asparagine
ASN1
Asparagine (coordinated with ZN)
ASP
Aspartic acid (deprotonated; charge -1)
ASPH
Aspartic acid (protonated; neutral)
CYS
Cysteine (deprotonated; charge -1/2)
CYSH
Cysteine (protonated; neutral)
CYS1
Cysteine (1st member of S-S bridge)
CYS2
Cysteine (2nd member of S-S bridge)
GLN
Glutamine
GLU
Glutamic acid (deprotonated; charge -1)
GLUH
Glutamic acid (protonated; neutral)
GLY
Glycine
HISA
Histidine (protonated at ND1; neutral)
HISB
Histidine (protonated at NE2; neutral)
HISH
Histidine (protonated at ND1 and NE2; charge +1)
HIS1
Histidine (coupled to HEME at NE2; neutral)
HIS2
Histidine (coupled to HEMC at NE2; neutral)
HYP
Hydroxyproline
ILE
Isoleucine
LEU
Leucine
LYS
Lysine (deprotonated; neutral)
LYSH
Lysine (protonated; charge +1)
MET
Methionine
PHE
Phenylalanine
PRO
Proline
SER
Serine
THR
Threonine
TRP
Tryptophan
TYR
Tyrosine
VAL
Valine
DALA
D-Alanine
ABU
L-2-amino-butanoic acid
AIB
-methylalanine
MEBMT
(4R)-4-[(E)-2-butanyl]-4, N-dimethyl-L-threonine
24
MELEU
MEVAL
SAR
N-methyl-L-leucine
N-methyl-L-valine
Sarcosine or N-methylglycine
nucleotides
DADE
DGUA
DCYT
DTHY
ADE
GUA
CYT
URA
2'-deoxyadenosine 5'-phosphoric acid |
2'-deoxyguanosine 5'-phosphoric acid | (DNA; charge -1)
2'-deoxycytidine 5'-phosphoric acid
|
2'-deoxythymidine 5'-phosphoric acid |
adenosine 5'-phosphoric acid
|
guanosine 5'-phosphoric acid
|(RNA; charge -1)
cytidine 5'-phosphoric acid
|
uridine 5'-phosphoric acid
|
FMNO
PFN
flavin mononucleotide (oxydized, deprotonated at FN5 and FN1; charge -1,
OPOHO2-)
flavin mononucleotide (semi-reduced, protonated at FN5; charge -1,
OPOHO2- )
flavin mononucleotide (reduced, protonated at FN5 and FN1; charge -1,
OPOHO2- )
proflavin (protonated at FN5; charge +1)
NADP
NADH
NDPH
NDPP
NDPHN
nicotinamide adenine dinucleotide (NAD+; charge -1)
nicotinamide adenine dinucleotide (NADH; charge -2)
nicotinamide adenine dinucleotide phosphate (NADPH; charge -3, OPOHO2-)
nicotinamide adenine dinucleotide phosphate (NADP+; charge -2, OPOHO2-)
nicotinamide adenine dinucleotide phosphate (NADPH; neutral, OPO(OH)2 )
sugars
GLCA
GLCB
GALA
GALB
MANA
MANB
TRH
UGLB
UMNB
UGAA
UGUA
 -D-glucopyranosyl (1-4 linkage; neutral)
-D-glucopyranosyl (1-4 linkage; neutral)
-D-galactopyranosyl (1-4 linkage; neutral)
-D-galactopyranosyl (1-4 linkage; neutral)
-D-mannoopyranosyl (1-4 linkage; neutral)
-D-mannoopyranosyl (1-4 linkage; neutral)
trehalose
-D-glucuronan (1-4 linkage; neutral)
-D-mannuronan (1-4 linkage; neutral)
-D-galacturonan (1-4 linkage; neutral)
-L-guluronan (1-4 linkage; neutral)
lipids
DPPC
Dipalmitoylphosphatidylcholine (neutral)
FMNS
FMNR
25
other molecules
HEME
heme group (charge -2, acidic groups deprotonated)
HEMC
heme group with bound CO (charge –2, acidic groups deprotonated)
CYT*
3',5'-O-(tetra isopropyl-1,3-disiloxanediyl) cytidine (neutral)
MTXH
FOL
DHF
THF
TMP
TMPH
TMPHP
methotrexate (protonated at N1; charge -2)
folate (charge -2)
7,8-dihydrofolate (charge -2)
5,6,7,8-tetrahydrofolate (charge -2)
trimethoprim (deprotonated at N1; neutral)
trimethoprim (protonated at N1; neutral)
trimethoprim (protonated at N1; charge +1)
PDG
ATP
3-phospho-D-glycerate (charge -2)
adenosine 5'-triphosphate (ATP; charge -3)
PMB
PMBH
BA
p-methylbenzyl alcoholate (charge -1)
p-methylbenzyl alcohol (neutral)
benzoic acid
RTOL
retinol (neutral)
TEMP
ETH
ETHH
tetramethyl pyrrolinyl (nitroxide spin label; neutral)
ethyl alcoholate (charge -1)
ethyl alcohol (neutral)
CH4
AR
methane (united atom)
argon
ions
SO42ZN2+
NA+
CLCA2+
MG2+
CU1+
CU2+
SO42- ion
zinc ion
sodium ion
chlorine ion
calcium ion
magnesium ion
copper ion
copper ion
(co)solvents
H2O
H2OE
CHCL3
DMSO
water (SPC model, rigid, [81.4] )
water (SPC/E model, rigid, [87.5] )
chloroform (rigid, [94.36] )
dimethylsulfoxide (rigid, [04.6] )
(charge -2)
(charge +2)
(charge +1)
(charge -1)
(charge +2)
(charge +2)
(charge +1)
(charge +2)
26
CH3OH
CCL4
TFE
UREA
methanol (rigid ) [00.9]
carbontetrachloride (rigid, [96.33] )
2,2,2-trifluoroethanol (flexible, [00.34])
Urea (flexible, [04.5])
27
Table 4.2.2
54A7 Solvent building blocks
Name
H2O
H2OE
H2OL
CHCL3
DMSO
CH3OH
CCL4
*)
Description
water (SPC model, [81.4])
water (SPC/E model, [87.5])
water (SPC/L model [02.18])*
chloroform ( [94.36] )
dimethylsulfoxide ( [04.6] )
methanol [00.9]
carbontetrachloride ( [96.33] )
There is no building block for SPC/L in the 53A5 force field, because it requires an additional atom
type. We suggest to use atom type 22 (DUM) for the hydrogens with van der Waals parameters
C6(22,22) ½ = 0.53 [kJ mol-1 nm6]½ and C12(22,22)½ = 0. The constraints should be set to rOH = 0.11 nm
and rHH = 0.173952 nm.
28
Table 4.2.3
54A7 End group building blocks
Name
Description
proteins and peptides
NH3+
N-terminus
NH2
N-terminus
NPRO
N-terminus for proline
COOO-terminus
COOH
O-terminus
(charge +1)
(neutral)
(charge +1)
(charge -1)
(neutral)
nucleic acids
D5OH
5’-terminal of DNA
D3OH
3’-terminal of DNA
3OH
3’-terminal of RNA
(neutral)
(neutral)
(neutral)
sugars
C1OH
C1OC
COHT
-C1-O1-H1 group for carbohydrates (neutral)
-C1-O1-CH3 group for carbohydrates
(neutral)
-Cn-On-Hon gropu for carbohydrates(neutral)
29