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Molecular Modeling and Bioinformatics Group

Entry: NAFlex_Circular30_1_CG


Nucleic Acid Data:


SequenceTCTCTCTCTCTCTCTCACCACCGCGTACAAGAAAGTTTGTTCTTTCATTTCGCCATACAGCTGCCTCGCGCGTTTCGGTGATATCGGTGAAAACCCTTCCCGTTTCGCTCAAGTTAGTATAAAAAAGCTGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATGCAGTCACTATGAATCAACTACTTAGATGGTATTAGTGACCTGTAACAGAGCTGAGGCATCTTTCTCAATGAAAGTGTCGGAACTCGGTACATAGGCTTCCGGCTGATAGTAGTCGTATACGACTACTATCAGCCGGAAGCCTATGTACCGAGTTCCGACACTTTCATTGAGAAAGATGCCTCAGCTCTGTTACAGGTCACTAATACCATCTAAGTAGTTGATTCATAGTGACTGCATATGTTGTGTTTTACAGTATTATGTAGTCTGTTTTTTATGCAAAATCTAATTTAATATATTGATATTTATATCATTTTACGTTTCTCGTTCAGCTTTTTTATACTAACTTGAGCGAAACGGGAAGGGTTTTCACCGATATCACCGAAACGCGCGAGGCAGCTGTATGGCGAAATGAAAGAACAAACTTTCTTGTACGCGGTGGTGAGAGAGAGAGAGAGA
Rev. Sequence-
TypeDNA
SubTypeB
Chainsduplex
Pdb-
LigandsNo
KeywordsDNA-B Duplex Naked


Simulation Metadata
Force FieldparmBSC1
Simulation Date0.00000000 1720396800
Simulated Time1,000
Time Step20 ps
PartsDNA
Temperature298K
WaterNo
Additional SolventNo
Counter IonsNo
Ionic ConcentrationNo
Additional IonsNo
Additional MoleculesNo
Ions ParametersNo
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorD.F.
Chainsduplex
CommentsCGeNArate: A Sequence-Dependent Coarse-Grained Model of DNA for Accurate Atomistic MD Simulations of kb-long Duplexes, DOI: 10.1093/nar/gkae444
CounterIonsNo
Formatmdcrd
FrameStep20 ps
Frames50000
IonicConcentrationNo
IonsParametersNo
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA
RMSd_avg35.112
RMSd_stdev6.870
Rgyr_avg147.607
Rgyr_stdev2.913
SASA_avg59739.459
SASA_stdev599.040
SubTypeB
Temperature298K
TopologyCircular30_1.pdb
TrajectoryCircular30_1.mdcrd
WaterNo
_idNAFlex_Circular30_1_CG
datasetArray
date0.00000000 1720396800
descriptionDNA-B Duplex Naked
forceFieldCGeNArate
ionsModel-
moleculeTypeDna
rev_sequence-
saltConcentration-
sequenceTCTCTCTCTCTCTCTCACCACCGCGTACAAGAAAGTTTGTTCTTTCATTTCGCCATACAGCTGCCTCGCGCGTTTCGGTGATATCGGTGAAAACCCTTCCCGTTTCGCTCAAGTTAGTATAAAAAAGCTGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATGCAGTCACTATGAATCAACTACTTAGATGGTATTAGTGACCTGTAACAGAGCTGAGGCATCTTTCTCAATGAAAGTGTCGGAACTCGGTACATAGGCTTCCGGCTGATAGTAGTCGTATACGACTACTATCAGCCGGAAGCCTATGTACCGAGTTCCGACACTTTCATTGAGAAAGATGCCTCAGCTCTGTTACAGGTCACTAATACCATCTAAGTAGTTGATTCATAGTGACTGCATATGTTGTGTTTTACAGTATTATGTAGTCTGTTTTTTATGCAAAATCTAATTTAATATATTGATATTTATATCATTTTACGTTTCTCGTTCAGCTTTTTTATACTAACTTGAGCGAAACGGGAAGGGTTTTCACCGATATCACCGAAACGCGCGAGGCAGCTGTATGGCGAAATGAAAGAACAAACTTTCTTGTACGCGGTGGTGAGAGAGAGAGAGAGA
soluteAtoms678
soluteCharge-
soluteResidues678
solventAtoms-
solventResidues-
time1,000
totalAtoms678
totalCharge-
totalIons-
totalResidues678
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-