ParmBSC1 forcefield Nucleotide MD Simulations Database

Simulations Table



SequenceFamilyOrigine / PDB idLength (ns)MD Simulation
↓ Normal B-DNA structures (including mismatches, epigenetic modifications and polymeric sequences) ↓
d(CGCGAATTCGCG)2B-DNA1BNA, 1NAJ10,000


1,200


800


2 x 1,000



d(CCATACaATACGG)2B-DNAMismatch AA, Fiber500
d(CCATACgATACGG)2B-DNAmismatch GG Fiber 500
d(CGCGA5mCGTCGCG)2 B-DNA 5methylC Fiber 250
d(CGCGA5hmCGTCGCG)2 B-DNA 5hydroxy-methylC Fiber 250
d(CGCGT5mCGACGCG)2 B-DNA 5methylC Fiber 500
d(CGCGACGTCGCG)2 B-DNA Fiber 500
d(CGCGTCGACGCG)2 B-DNA Fiber 500
d(GCCTATAAACGCCTATAA)2 B-DNA Fiber 1,000
d(CTAGGTGGATGACTCATT)2 B-DNA Fiber 1,000
d(CACGGAACCGGTTCCGTG)2 B-DNA Fiber 1,000
d(GCCGAGCGAGCGAGCGGC)2 B-DNA Fiber 1,000
d(GCCTAGCTAGCTAGCTGC)2 B-DNA Fiber 1,000
d(GCTGCGTGCGTGCGTGGC)2 B-DNA Fiber 1,000
d(GCGATCGATCGATCGAGC)2 B-DNA Fiber 1,000
d(GCGAGGGAGGGAGGGAGC)2 B-DNA Fiber 1,000
d(GCGCGGGCGGGCGGGCGC)2 B-DNA Fiber 1,000
d(GCGGGGGGGGGGGGGGGC)2 B-DNA Fiber 1,000
d(GCGTGGGTGGGTGGGTGC)2 B-DNA Fiber 1,000
d(CTCGGCGCCATC)2 B-DNA 2HKB 590
d(CCTCTGGTCTCC)2 B-DNA 2K0V 590
d(CGCATGCTACGC)2 B-DNA 2L8Q 590
d(GGATATATCC)2 B-DNA 2LWG 590
d(GCGCATGCTACGCG)2 B-DNA 2M2C 590
d(CCTCAGGCCTCC)2 B-DNA 2NQ1 590
d(CGCGAAAAAACG)2 B-DNA (A-track) 1D89 200
d(GGCAAAAAACGG)2 B-DNA (A-track)1FZX 200
d(GCAAAATTTTGC)2 B-DNA (A-track)1RVH 200
d(CTTTTAAAAG)2 B-DNA (A-track)1SK5 200
d(AGGGGCCCCT)2 B-DNA (A-track)440D 200
d(GGCAAGAAACGG)2 B-DNA (A-track)1G14 1,000
d(CGATCGATCG)2 B-DNA crystal1D23 32 x 2,000 Available upon request to the author (Prof. D.A. Case)
↓ Longer Oligomers (> 30 base-pairs) ↓
SequenceFamilyOrigine / PDB idLength (ns)MD Simulation
d(ATGGATCCATAGACCAGAACATGATGTTCTCA)2 B-DNA 32mer Fiber 1,000
d(CGCGATTGCCTAACGAGTACTCGTTAGGCAATCGCG)2 B-DNA 36mer Fiber 2 x 300
d(CGCGATTGCCTAACGGACAGGCATAGACGTCTATGCCTGTCCGTTAGGCAATCGCG)2 B-DNA 56mer Fiber 1 x 290
1 x 500
d(CGTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGCG)2 B-DNA 56mer Fiber 300
d(CGCCGGCAGTAGCCGAAAAAATAGGCGCGCGCTCAAAAAAATGCCCCATGCCGCGC)2 B-DNA 56mer Fiber 1 x 360
1 x 440
1 x 500

d(ATCTTTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGAT)2 106-mer circle 10 turns (reg A) Fiber 100
d(ATCTTTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGAT)2 106-mer circle 10 turns (reg B) Fiber 100
d(ATCTTTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGAT)2 106-mer circle 10 turns (reg C) Fiber 100
d(ATCTTTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGAT)2 106-mer circle 9 turns Fiber 50
d(ATCTTGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGTTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGAT)2 100-mer circle 9 turns Fiber 100
↓ Complexes of DNA with proteins or drugs ↓
SequenceFamilyOrigine / PDB idLength (ns)MD Simulation
147mer nucleosome DNA-histones1KX5 500
DNA:HU complex DNA-HU protein1P71 1,000
DNA:HU complex DNA-HU protein1P71 (without mismatches) 1,000
DNA:TRP repressor DNA-repressor1TRO 1,000
DNA:leucine zipper DNA-transc factor2DGC 1,000
DNA:P22 c2 DNA-represor3JXC 1,000
d(CGCAAATTTGCG)2-distamycin DNA-mG binder2DND 700
d(CTTTTCGAAAAG) 2-Hoescht Drug cooperativity1QSX 10 x 10 Available upon request to the author (Prof. C. Laughton)
d(CGTACG)2-daunomycin DNA-intercalator1D11 600
↓ Unusual DNA structures ↓
SequenceFamilyOrigine / PDB idLength (ns)MD Simulation
d(GGGG)4PS quadruplex
(Without Thymine Loops)		352D 440
d(GGGG)4APS quadruplex
(Without Thymine Loops)		156D 440
d(T•A•T)10PS triplexFiber 440
d(G•G•C)10PS triplexFiber 440
d(G•G•C)10APS triplexFiber 440
d(ATATATATATAT)2 H-duplex1GQU 720
d(CGATATATATAT)2 H-duplex2AF1 400
d(AAGGGTGGGTGTAAGTGTGGGTGGGT)G_quadruplex2LPW 5,000
d(AGGGTTAGGGTTAGGGTTAGGG)G-loop quadruplex (HTQ)1KF1 1,000
d(GGGGTTTTGGGG)2 G quadruplex (OxyQ)1JRN 1,000
d(CCGGTACCGG)4Holliday Junction1DCW 1,000
d(CGCGCGCGCG)2 Z-DNA, duplex1I0T 2 x 385
↓ Dynamic Transitions ↓
SequenceFamilyOrigine / PDB idLength (ns)MD Simulation
d(GCGAAGC)Hairpin fold (REXMD)*1PQT 1,000
d(CGCGAATTCGCG)2 A-form in ethanol1BNA 200
d(CGCGAATTCGCG)2 A->B transition (H2O) 1BNA 5 x 40
d(GGCGCC)2 DNA unfolding (Pyridine) 1P25 400
↓ ParmBSC1 validation: Drew-Dickerson Dodecamer with different force-fields / salt concentration ↓
SequenceFamilyOrigine / PDB idLength (ns)MD Simulation
d(CGCGAATTCGCG)2B-DNA1BNA, 1NAJ
10,000 (parmBSC1)


1,500 (parmBSC0)


1,500 (OL1)


1,500 (OL4)


1,500 (OL1+OL4)


1,500 (Cheng-Garcia)


1,500 (Charmm36)


2,000 (0.15mM)


3,000 (0.5mM)








↓ ParmBSC1 benchmarking: Drew-Dickerson Dodecamer with different HPC environments ↓
SequenceFamilyOrigine / PDB idLength (ns)MD Simulation
d(CGCGAATTCGCG)2B-DNA1BNA, 1NAJ
100 (Amber-GPU)


100 (Amber-CPU)


100 (Gromacs-GPU)


100 (Gromacs-CPU)



(*) Only final frames corresponding to folded state are shown

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