Amber prep files for a neutral Arginine residue, Arn
Constructed by Aaron Weis, Pär
Söderhjelm and Ulf Ryde, 13/10-05
Ulf.Ryde .at. teokem.lu.se
- Took an Arg residue in avidin.
- Protonated it with Amber
- Deleted the HH22 atom (a calculation at the B3LYP/6-311+G(2d,2p)
level showed that this was ~2 kJ/mole more stable than removal of the
HE atom).
- Optimised it with HF/6-31G*
- Calculated MK ESP points by Gaussian-98 and various methods and
basis sets.
- Calcualted RESP charges by Antechamber
- Inserted the charges in a standard Arg residue, deleting the HH22
atom.
- Corrected the charges to neutral on atom CA.
Force-field 1994 (HF/6-31G* charges):
arn94.in
0 0 2
This is neutral ARG for AMBER-94
force field (HF/6-31G*); AW
& UR 13/10-05;
corrected char
ge on CA: 0.05461
molecule.res
ARN INT 0
CORRECT
OMIT DU BEG
0.0000
1 DUMM
DU M 0 -1
-2 0.000
.0
.0 .00000
2 DUMM
DU M 1 0
-1 1.449
.0
.0 .00000
3 DUMM
DU M 2 1
0 1.522
111.1
.0 .00000
4
N N M
8 4 3 1.362
116.304 58.313 -0.61425
5
H H E
4 8 4 1.020
119.088 6.079 0.37526
6
CA CT M
4 8 4 1.469
123.073 -176.692 -0.04834
7
HA H1 E
6 4 8 1.104
105.652 32.227 0.09546
8
CB CT 3
6 4 8 1.536
110.845 152.442 0.02335
9
HB2 HC E 8
6 4 1.104
108.632 61.963 0.03300
10 HB3
HC E 8 6
4 1.102 107.566
175.665 0.03300
11
CG CT 3
8 6 4 1.540
114.958 -61.436 0.15920
12 HG2
HC E 11 8
6 1.105 110.319
57.877 -0.05893
13 HG3
HC E 11 8
6 1.104 108.370
174.272 -0.05893
14
CD CT 3 11
8 6 1.543
115.045 -64.289 0.20895
15 HD2
H1 E 14 11
8 1.101 110.885
63.034 0.02506
16 HD3
H1 E 14 11
8 1.102 109.209
179.127 0.02506
17
NE N2 B 14
11 8 1.473
115.372 -57.634 -0.86040
18
HE H E 17
14 11 1.019
114.462 79.854 0.37571
19
CZ CA B 17
14 11 1.393
124.133 -65.311 0.91886
20 NH1
N2 B 19 17
14 1.397 115.010
-25.925 -0.91983
21 HH11
H E 20 19
17 1.022 115.181
-37.403 0.39274
22 HH12
H E 20 19
17 1.022 110.896
-164.585 0.39274
23 NH2
N2 S 19 17
14 1.306 125.633
154.428 -0.94281
24 HH21
H E 23 19
17 1.030 109.610
-8.049 0.35919
25
C C M
6 4 8 1.560
111.173 -83.297 0.68923
26
O O E
25 6 4
1.244 122.848 -114.814 -0.60332
IMPROPER
-M
CA N H
CA
+M C O
NE NH1
CZ NH2
CD
CZ NE HE
CZ HH11
NH1 HH12
DONE
STOP
Force-field 2003 (B3LYP/cc-pVTZ SCRF=(IEFPCM,eps=4) charges):
arn03.in
0 0 2
This is neutral ARG for AMBER-03
force field (B3LYP/cc-pVTZ SCRF=(IEFPCM,eps=4) charges); AW & UR
13/10-05; corrected charge on CA: 0.03839
molecule.res
ARN INT 0
CORRECT
OMIT DU BEG
0.0000
1 DUMM
DU M 0 -1
-2 0.000
.0
.0 .00000
2 DUMM
DU M 1 0
-1 1.449
.0
.0 .00000
3 DUMM
DU M 2 1
0 1.522
111.1
.0 .00000
4
N N M
8 4 3 1.362
116.304 58.313 -0.50752
5
H H E
4 8 4 1.020
119.088 6.079 0.38539
6
CA CT M
4 8 4 1.469
123.073 -176.692 -0.04495
7
HA H1 E
6 4 8 1.104
105.652 32.227 0.13845
8
CB CT 3
6 4 8 1.536
110.845 152.442 0.04567
9
HB2 HC E 8
6 4 1.104
108.632 61.963 0.00791
10 HB3
HC E 8 6
4 1.102 107.566
175.665 0.00791
11
CG CT 3
8 6 4 1.540
114.958 -61.436 0.20197
12 HG2
HC E 11 8
6 1.105 110.319
57.877 -0.06030
13 HG3
HC E 11 8
6 1.104 108.370
174.272 -0.06030
14
CD CT 3 11
8 6 1.543
115.045 -64.289 0.03559
15 HD2
H1 E 14 11
8 1.101 110.885
63.034 0.07662
16 HD3
H1 E 14 11
8 1.102 109.209
179.127 0.07662
17
NE N2 B 14
11 8 1.473
115.372 -57.634 -0.73792
18
HE H E 17
14 11 1.019
114.462 79.854 0.38534
19
CZ CA B 17
14 11 1.393
124.133 -65.311 0.80800
20 NH1
N2 B 19 17
14 1.397 115.010
-25.925 -0.81318
21 HH11
H E 20 19
17 1.022 115.181
-37.403 0.37498
22 HH12
H E 20 19
17 1.022 110.896
-164.585 0.37498
23 NH2
N2 S 19 17
14 1.306 125.633
154.428 -1.04271
24 HH21
H E 23 19
17 1.030 109.610
-8.049 0.40178
25
C C M
6 4 8 1.560
111.173 -83.297 0.56363
26
O O E
25 6 4
1.244 122.848 -114.814 -0.61796
IMPROPER
-M
CA N H
CA
+M C O
NE NH1
CZ NH2
CD
CZ NE HE
CZ HH11
NH1 HH12
DONE
STOP
Force-field 2002 (B3LYP/cc-pVTZ charges):
arn02.in
0 0 2
This is neutral ARG for AMBER-02
polarisable force field (B3LYP/cc-pVTZ charges); AW & UR 13/10-05; corrected charge on CA:
0.07112
molecule.res
ARN INT 0
CORRECT
OMIT DU BEG
0.0000
1 DUMM
DU M 0 -1
-2 0.000
.0
.0 .00000
2 DUMM
DU M 1 0
-1 1.449
.0
.0 .00000
3 DUMM
DU M 2 1
0 1.522
111.1
.0 .00000
4
N N M
8 4 3 1.362
116.304 58.313 -0.47578
5
H H E
4 8 4 1.020
119.088 6.079 0.32834
6
CA CT M
4 8 4 1.469
123.073 -176.692 -0.07824
7
HA H1 E
6 4 8 1.104
105.652 32.227 0.08795
8
CB CT 3
6 4 8 1.536
110.845 152.442 0.06700
9
HB2 HC E 8
6 4 1.104
108.632 61.963 0.02262
10 HB3
HC E 8 6
4 1.102 107.566
175.665 0.02262
11
CG CT 3
8 6 4 1.540
114.958 -61.436 0.16150
12 HG2
HC E 11 8
6 1.105 110.319
57.877 -0.06510
13 HG3
HC E 11 8
6 1.104 108.370
174.272 -0.06510
14
CD CT 3 11
8 6 1.543
115.045 -64.289 0.16804
15 HD2
H1 E 14 11
8 1.101 110.885
63.034 0.02635
16 HD3
H1 E 14 11
8 1.102 109.209
179.127 0.02635
17
NE N2 B 14
11 8 1.473
115.372 -57.634 -0.72139
18
HE H E 17
14 11 1.019
114.462 79.854 0.33436
19
CZ CA B 17
14 11 1.393
124.133 -65.311 0.71817
20 NH1
N2 B 19 17
14 1.397 115.010
-25.925 -0.72837
21 HH11
H E 20 19
17 1.022 115.181
-37.403 0.33126
22 HH12
H E 20 19
17 1.022 110.896
-164.585 0.33126
23 NH2
N2 S 19 17
14 1.306 125.633
154.428 -0.82940
24 HH21
H E 23 19
17 1.030 109.610
-8.049 0.32287
25
C C M
6 4 8 1.560
111.173 -83.297 0.54246
26
O O E
25 6 4
1.244 122.848 -114.814 -0.52777
IMPROPER
-M
CA N H
CA
+M C O
NE NH1
CZ NH2
CD
CZ NE HE
CZ HH11
NH1 HH12
DONE
STOP