|
Id. |
PDB |
Type |
SubType |
ForceField |
Solvent |
Description |
Time (ns) |
Sequence |
|
NAFlex_DDD_bsc1 |
1NAJ |
Dna |
B |
parmBSC0 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC0 TIP3P Electroneutral |
10,000 |
CGCGAATTCGCG |
|
NAFlex_D05M |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
3,000 |
CGCGAATTCGCG |
|
NAFlex_DTipDang015M |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
2,000 |
CGCGAATTCGCG |
|
NAFlex_BSC1-BSC0 |
1NAJ |
Dna |
B |
parmBSC0 |
TIP3P |
DNA-B Duplex Naked TIP3P Electroneutral ParmBSC0 |
1,500 |
CGCGAATTCGCG |
|
NAFlex_BSC1-C36 |
1NAJ |
Dna |
B |
Charmm36 |
TIP3P |
DNA-B Duplex Naked Charmm36 TIP3P Electroneutral |
1,500 |
CGCGAATTCGCGCGCGAATTCGCG |
|
NAFlex_BSC1-Garcia |
1NAJ |
Dna |
B |
ParmBSC0-CG |
TIP3P |
DNA-B Duplex Naked Cheng-Garcia TIP3P Electroneutral |
1,500 |
CGCGAATTCGCG |
|
NAFlex_BSC1-OL1 |
1NAJ |
Dna |
B |
ParmBSC0-OL1 |
TIP3P |
DNA-B Duplex Naked OL1 TIP3P Electroneutral |
1,500 |
CGCGAATTCGCG |
|
NAFlex_BSC1-OL1-OL4 |
1NAJ |
Dna |
B |
ParmBSC0-OL1-OL4 |
TIP3P |
DNA-B Duplex Naked OL1+OL4 TIP3P Electroneutral |
1,500 |
CGCGAATTCGCG |
|
NAFlex_BSC1-OL4 |
1NAJ |
Dna |
B |
ParmBSC0-OL4 |
TIP3P |
DNA-B Duplex Naked OL4 TIP3P Electroneutral |
1,500 |
CGCGAATTCGCG |
|
NAFlex_DDD_II |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
1,200 |
CGCGAATTCGCG |
|
NAFlex_DDD_II_1 |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
1,000 |
CGCGAATTCGCG |
|
NAFlex_DDD_II_2 |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
1,000 |
CGCGAATTCGCG |
|
NAFlex_DSpcCheatham |
1BNA |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E Electroneutral |
1,000 |
CGCGAATTCGCG |
|
NAFlex_DSpcDang |
1BNA |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E Electroneutral |
1,000 |
CGCGAATTCGCG |
|
NAFlex_DTipCheatham |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
1,000 |
CGCGAATTCGCG |
|
NAFlex_muAGTC |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCTCAGTCAGTCAGTCGC |
|
NAFlex_muTGTC |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCTCTGTCTGTCTGTCGC |
|
NAFlex_DDD_800ns |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
800 |
CGCGAATTCGCG |
|
NAFlex_56merTIP3P |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
500 |
CGCGATTGCCTAACGGACAGGCATAGACGTCTATGCCTGTCCGTTAGGCAATCGCG |
|
NAFlex_ACGT |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
500 |
CGCGACGTCGCG |
|
NAFlex_CTAG_21 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGAGACTAGACTCGC |
|
NAFlex_CTAG_22 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGAGACTAGCCTCGC |
|
NAFlex_CTAG_23 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGAGACTAGGCTCGC |
|
NAFlex_CTAG_24 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGAGACTAGTCTCGC |
|
NAFlex_CTAG_25 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGAGCCTAGACTCGC |
|
NAFlex_CTAG_26 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGAGCCTAGCCTCGC |
|
NAFlex_CTAG_27 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGAGCCTAGGCTCGC |
|
NAFlex_CTAG_28 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGAGGCTAGACTCGC |
|
NAFlex_CTAG_29 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGAGGCTAGCCTCGC |
|
NAFlex_CTAG_30 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGAGTCTAGACTCGC |
|
NAFlex_colibactin1 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked TIP3P Electroneutral |
400 |
CGCGAAAATTTTCGCG |
|
NAFlex_36merSPCE |
NONE |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E Electroneutral |
300 |
CGCGATTGCCTAACGAGTACTCGTTAGGCAATCGCG |
|
NAFlex_36merTIP3P |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
300 |
CGCGATTGCCTAACGAGTACTCGTTAGGCAATCGCG |
|
NAFlex_56merSPCE |
NONE |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E Electroneutral |
290 |
CGCGATTGCCTAACGGACAGGCATAGACGTCTATGCCTGTCCGTTAGGCAATCGCG |
|
NAFlex_ACGThmet |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked Parm99 TIP3P AddedSalt |
250 |
CGCGAXGTCGCG |
|
NAFlex_ACGTmet |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked Parm99 TIP3P AddedSalt |
250 |
CGCGAXGTCGCG |
|
NAFlex_A-Ethanol |
1BNA |
Dna |
A (in ethanol) |
parmBSC1 |
Wat-Ethanol |
DNA-A Duplex Naked ParmBSC1 Water-Ethanol Electroneutral |
200 |
CGCGAATTCGCG |
|
NAFlex_TT_DZ1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXTAACGCACGXTCGCGCTGTCXTCCGCGTTTXTACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_SSB1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXTAACGCACGXTCGCGCTGTCXTCCGCGTTTXTACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_TG1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXTAACGCACGXTCGCGCTGTCXTCCGCGTTTXTACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_noalch1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXTAACGCACGXTCGCGCTGTCXTCCGCGTTTXTACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_v106Bt10 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked Parm99 TIP3P AddedSalt |
100 |
TGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGATATCTT |
|
NAFlex_v106Ct10 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked Parm99 TIP3P AddedSalt |
100 |
GAGGATATCTTTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGT |
|
NAFlex_v106R2t10 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked Parm99 TIP3P AddedSalt |
100 |
ATCTTTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGAT |
|
NAFlex_v106R3t10 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked Parm99 TIP3P AddedSalt |
100 |
ATCTTTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGAT |
|
NAFlex_v106t10 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked Parm99 TIP3P AddedSalt |
100 |
ATCTTTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGAT |
|
NAFlex_DDD_GMX_CPU |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
100 |
CGCGAATTCGCG |
|
NAFlex_DDD_GMX_GPU |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
100 |
CGCGAATTCGCG |
|
NAFlex_DDD_Amber_CPU |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
100 |
CGCGAATTCGCG |
|
NAFlex_DDD_Amber_GPU |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
100 |
CGCGAATTCGCG |
|
NAFlex_v106t9 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked Parm99 TIP3P AddedSalt |
50 |
ATCTTTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGAT |
|
NAFlex_A2B_1 |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-Mixed Duplex Naked ParmBSC1 TIP3P Electroneutral Transition |
40 |
CGCGAATTCGCG |
|
NAFlex_A2B_2 |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-Mixed Duplex Naked ParmBSC1 TIP3P Electroneutral Transition |
40 |
CGCGAATTCGCG |
|
NAFlex_A2B_3 |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-Mixed Duplex Naked ParmBSC1 TIP3P Electroneutral Transition |
40 |
CGCGAATTCGCG |
|
NAFlex_A2B_4 |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-Mixed Duplex Naked ParmBSC1 TIP3P Electroneutral Transition |
40 |
CGCGAATTCGCG |
|
NAFlex_A2B_5 |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-Mixed Duplex Naked ParmBSC1 TIP3P Electroneutral Transition |
40 |
CGCGAATTCGCG |
