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Molecular Modeling and Bioinformatics Group

Entry: NAFlex_miniABC_Na_2


Nucleic Acid Data:


SequenceGCAATAAGTACCAGGAGC
Rev. SequenceGCTCCTGGTACTTATTGC
TypeDNA
SubTypeB
Chainsduplex
Pdb-
LigandsNo
KeywordsB-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl


Simulation Metadata
Force FieldparmBSC1
Simulation Date0.00000000 1457654400
Simulated Time1,000
Time Step1 ps
PartsDNA+ions
Temperature298K
WaterSPC/E
Additional SolventNo
Counter IonsNa+
Ionic ConcentrationElectroneutrality
Additional IonsNo
Additional MoleculesNo
Ions ParametersDang
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorP.D.
Chainsduplex
CommentsminiABC project, Na collection
CounterIonsNa+
Formatcrd
FrameStep1 ps
Frames1000000
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA+ions
SubTypeB
Temperature298K
TopologyminiABC_2.Na.ions.top
TrajectoryminiABC_2.Na.ions.1000ns.trj
WaterSPC/E
_idNAFlex_miniABC_Na_2
boxAngle109.471219
boxX75.003
boxY75.003
boxZ75.003
datasetArray
date0.00000000 1457654400
descriptionB-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceGCTCCTGGTACTTATTGC
saltConcentration-
sequenceGCAATAAGTACCAGGAGC
soluteAtoms1141
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1141
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-