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Molecular Modeling and Bioinformatics Group

Entry: NAFlex_miniABC_NaK_3


Nucleic Acid Data:


SequenceGCAGAAACAGCTCTGCGC
Rev. SequenceGCGCAGAGCTGTTTCTGC
TypeDNA
SubTypeB
Chainsduplex
Pdb-
LigandsNo
KeywordsB-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl/KCl 50%/50%


Simulation Metadata
Force FieldparmBSC1
Simulation Date0.00000000 1457740800
Simulated Time1,000
Time Step1 ps
PartsDNA+ions
Temperature298K
WaterSPC/E
Additional SolventNo
Counter IonsK+,Na+
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, NaK collection
CounterIonsK+,Na+
Formatcrd
FrameStep1 ps
Frames1000000
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA+ions
SubTypeB
Temperature298K
TopologyminiABC_3.NaK.ions.top
TrajectoryminiABC_3.NaK.ions.1000ns.trj
WaterSPC/E
_idNAFlex_miniABC_NaK_3
boxAngle109.471219
boxX75.012
boxY75.012
boxZ75.012
datasetArray
date0.00000000 1457740800
descriptionB-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl/KCl 50%/50%
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceGCGCAGAGCTGTTTCTGC
saltConcentration-
sequenceGCAGAAACAGCTCTGCGC
soluteAtoms1139
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1139
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-