|
Id. |
PDB |
Type |
SubType |
ForceField |
Solvent |
Description |
Time (ns) |
Sequence |
|
NAFlex_ProtDNA_1a0a |
1A0A |
Prot-Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
2,000 |
CTAGTCCCACGTGTGAG |
|
NAFlex_1tro |
1TRO |
Prot-Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Complex ParmBSC1 SPC/E AddedSalt Prot-nuc Overhanging-bases |
1,000 |
GTACTAGTTAACTAGTAC |
|
NAFlex_AGCT |
NONE |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E AddedSalt |
1,000 |
GCCTAGCTAGCTAGCTGC |
|
NAFlex_lks2 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
1,000 |
CTAGGTGGATGACTCATT |
|
NAFlex_muAGCT |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCCTAGCTAGCTAGCTGC |
|
NAFlex_muGATA |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCTAGATAGATAGATAGC |
|
NAFlex_miniABC_NaK_13 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl/KCl 50%/50% |
1,000 |
GCTTGTGACGGCTAGGGC |
|
NAFlex_miniABC_K_13 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol KCl |
1,000 |
GCTTGTGACGGCTAGGGC |
|
NAFlex_miniABC_Na_13 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl |
1,000 |
GCTTGTGACGGCTAGGGC |
|
NAFlex_miniABC_13_CG |
NONE |
Dna |
B |
CGeNArate |
No |
DNA-B Duplex Naked |
1,000 |
GCTTGTGACGGCTAGGGC |
|
NAFlex_CTAG_CG |
NONE |
Dna |
B |
CGeNArate |
No |
DNA-B Duplex Naked |
1,000 |
CGCTCTCTAGAGAGGC |
|
NAFlex_AGCT_CG |
NONE |
Dna |
B |
CGeNArate |
No |
DNA-B Duplex Naked |
1,000 |
GCCTAGCTAGCTAGCTGC |
|
NAFlex_CTAG_1 |
NONE |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E AddedSalt |
500 |
CGTCGGCTAGCCGAGC |
|
NAFlex_CTAG_10 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGCGCGCTAGCGCGGC |
|
NAFlex_CTAG_11 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTACTAGAGAGGC |
|
NAFlex_CTAG_12 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTACTAGCGAGGC |
|
NAFlex_CTAG_13 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTACTAGGGAGGC |
|
NAFlex_CTAG_15 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTCCTAGAGAGGC |
|
NAFlex_CTAG_16 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTCCTAGCGAGGC |
|
NAFlex_CTAG_17 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTCCTAGGGAGGC |
|
NAFlex_CTAG_18 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTGCTAGAGAGGC |
|
NAFlex_CTAG_19 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTGCTAGCGAGGC |
|
NAFlex_CTAG_2 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTCCTAGGAGAGC |
|
NAFlex_CTAG_20 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTTCTAGAGAGGC |
|
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_3 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGAAAACTAGAAAAGC |
|
NAFlex_CTAG_30 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGAGTCTAGACTCGC |
|
NAFlex_CTAG_31 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGCTAGCTAGCTAGGC |
|
NAFlex_CTAG_32 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGCTAGCTAGCTAGGC |
|
NAFlex_CTAG_4 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGAAAACTAGTTTTGC |
|
NAFlex_CTAG_5 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGATATCTAGATATGC |
|
NAFlex_CTAG_6 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTATACTAGTATAGC |
|
NAFlex_CTAG_7 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGGGGCTAGGGGGGC |
|
NAFlex_CTAG_8 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGGGGCTAGCCCCGC |
|
NAFlex_CTAG_9 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGGCGCCTAGGCGCGC |
|
NAFlex_CTAG_flex |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGCTCTCTAGAGAGGC |
|
NAFlex_CTAG_rig |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGCAAGCTAGCTTGGC |
|
NAFlex_CTAG_14 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTACTAGTGAGGC |
|
NAFlex_CG_OG1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTCXAACGCACGCXCGCGCTGTCCXCCGCGTTTCXACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_CG_OG2 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACXGCTTAAACCXACGTACGCGCXGTCCCCCGCXTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_CG_5hmC1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXGAACGCACGXGCGCGCTGTCXGCCGCGTTTXGACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_CG_5hmC2 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCAXGGCTTAAACXGACGTACGCGXGGTCCCCCGXGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_CG_5mC1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXGAACGCACGXGCGCGCTGTCXGCCGCGTTTXGACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_CG_5mC2 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCAXGGCTTAAACXGACGTACGCGXGGTCCCCCGXGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_CG_noalch1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTCGAACGCACGCGCGCGCTGTCCGCCGCGTTTCGACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_CG_noalch2 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACGGCTTAAACCGACGTACGCGCGGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_DZ1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXTAACGCACGXTCGCGCTGTCXTCCGCGTTTXTACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_DZ2 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCAXTGCTTAAACXTACGTAC |
|
NAFlex_TT_PP1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXXAACGCACGXXCGCGCTGTCXXCCGCGTTTXXACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_PP2 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCAXXGCTTAAACXXACGTACGCGXXGTCCCCCGXXTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_SSB1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXTAACGCACGXTCGCGCTGTCXTCCGCGTTTXTACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_SSB2 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCAXTGCTTAAACXTACGTACGCGXTGTCCCCCGXTTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_TG1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXTAACGCACGXTCGCGCTGTCXTCCGCGTTTXTACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_TT1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXXAACGCACGXXCGCGCTGTCXXCCGCGTTTXXACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_TT2 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCAXXGCTTAAACXXACGTACGCGXXGTCCCCCGXXTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_noalch1 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXTAACGCACGXTCGCGCTGTCXTCCGCGTTTXTACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
|
NAFlex_TT_noalch2 |
- |
Dna |
B |
parmBSC1 |
TIP3P |
-B Duplex Naked TIP3P Electroneutral |
200 |
XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCAXTGCTTAAACXTACGTAC |