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Simulation report and files

General information

Name: NSP16 in aqueous solution

Included proteins: NSP16

Uniprot ID: P0DTD1

Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)

PDB ID: 6W4H

Submitted by: Institut Hospital del Mar d'Investigacions Mèdiques

Submission date: March 04, 2021

System setup

Ligands: None

Membrane composition: None

Solvent type: TIP3P

Total number of atoms: 108754

Simulation details

Software and version: AceMD 3.2.3

Forcefield and version: CHARMM36 2019

Time step : 4.0 fs

Delta : 0.4 ns

Replicates: 1

Accumulated simulation time: 1.0000 µs



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NSP16 in aqueous solution ( 6W4H)

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Hydrogen bonds

RMSD
Trajectory:
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Selection:
Protein alpha carbons
Protein CA, CB, C, N, O
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RMSF
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Frames:
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From to
Stride:
Selection:
Protein alpha carbons
Protein CA, CB, C, N, O
Non-hydrogen protein atoms
All protein atoms
Variant impact

Select a variant from the sequence to obtain its impact score as well as mutation effect and time-dependent descriptors:

Display isolate: All isolates
NSP16
AA
Seq. pos.
PDB resID
S
1
6799
S
2
6800
Q
3
6801
A
4
6802
W
5
6803
Q
6
6804
P
7
6805
G
8
6806
V
9
6807
A
10
6808
M
11
6809
P
12
6810
N
13
6811
L
14
6812
Y
15
6813
K
16
6814
M
17
6815
Q
18
6816
R
19
6817
M
20
6818
L
21
6819
L
22
6820
E
23
6821
K
24
6822
C
25
6823
D
26
6824
L
27
6825
Q
28
6826
N
29
6827
Y
30
6828
G
31
6829
D
32
6830
S
33
6831
A
34
6832
T
35
6833
L
36
6834
P
37
6835
K
38
6836
G
39
6837
I
40
6838
M
41
6839
M
42
6840
N
43
6841
V
44
6842
A
45
6843
K
46
6844
Y
47
6845
T
48
6846
Q
49
6847
L
50
6848
C
51
6849
Q
52
6850
Y
53
6851
L
54
6852
N
55
6853
T
56
6854
L
57
6855
T
58
6856
L
59
6857
A
60
6858
V
61
6859
P
62
6860
Y
63
6861
N
64
6862
M
65
6863
R
66
6864
V
67
6865
I
68
6866
H
69
6867
F
70
6868
G
71
6869
A
72
6870
G
73
6871
S
74
6872
D
75
6873
K
76
6874
G
77
6875
V
78
6876
A
79
6877
P
80
6878
G
81
6879
T
82
6880
A
83
6881
V
84
6882
L
85
6883
R
86
6884
Q
87
6885
W
88
6886
L
89
6887
P
90
6888
T
91
6889
G
92
6890
T
93
6891
L
94
6892
L
95
6893
V
96
6894
D
97
6895
S
98
6896
D
99
6897
L
100
6898
N
101
6899
D
102
6900
F
103
6901
V
104
6902
S
105
6903
D
106
6904
A
107
6905
D
108
6906
S
109
6907
T
110
6908
L
111
6909
I
112
6910
G
113
6911
D
114
6912
C
115
6913
A
116
6914
T
117
6915
V
118
6916
H
119
6917
T
120
6918
A
121
6919
N
122
6920
K
123
6921
W
124
6922
D
125
6923
L
126
6924
I
127
6925
I
128
6926
S
129
6927
D
130
6928
M
131
6929
Y
132
6930
D
133
6931
P
134
6932
K
135
6933
T
136
6934
K
137
6935
N
138
6936
V
139
6937
T
140
6938
K
141
6939
E
142
6940
N
143
6941
D
144
6942
S
145
6943
K
146
6944
E
147
6945
G
148
6946
F
149
6947
F
150
6948
T
151
6949
Y
152
6950
I
153
6951
C
154
6952
G
155
6953
F
156
6954
I
157
6955
Q
158
6956
Q
159
6957
K
160
6958
L
161
6959
A
162
6960
L
163
6961
G
164
6962
G
165
6963
S
166
6964
V
167
6965
A
168
6966
I
169
6967
K
170
6968
I
171
6969
T
172
6970
E
173
6971
H
174
6972
S
175
6973
W
176
6974