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Molecular Modeling and Bioinformatics Group

Entry: NAFlex_RNA_miniABC_KCl_12


Nucleic Acid Data:


SequenceGCUGGCAUGAAGCGACGC
Rev. SequenceGCGUCGCUUCAUGCCAGC
TypeRNA
SubTypeA
Chainsduplex
Pdb-
LigandsNo
KeywordsRNA-A Duplex Naked TIP3P AddedSalt


Simulation Metadata
Force FieldparmBSC1
Simulation Date0.00000000 1662595200
Simulated Time1,000
Time Step20 ps
PartsRNA+ions
Temperature298K
WaterTIP3P
Additional SolventNo
Counter IonsK+
Ionic Concentration0.15 M
Additional IonsKCl
Additional MoleculesNo
Ions ParametersDang
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsKCl
AdditionalMoleculesNo
AdditionalSolventNo
AuthorA.H.
Chainsduplex
CommentsminiABC project, RNA collection
CounterIonsK+
Formatnc
FrameStep20 ps
Frames1000000
IonicConcentration0.15 M
IonsParametersDang
LigandsNo
NucTypeRNA
PDBNONE
PartsRNA+ions
RMSd_avg4.060
RMSd_stdev0.674
Rgyr_avg16.630
Rgyr_stdev0.539
SASA_avg6560.591
SASA_stdev99.684
SubTypeA
Temperature298K
TopologyGCUGGCAUGAAGCGACGC.dry.parmtop
TrajectoryGCUGGCAUGAAGCGACGC.dry.5000.nc
WaterTIP3P
_idNAFlex_RNA_miniABC_KCl_12
boxAngle109.471219
boxX82.5337432
boxY82.5337432
boxZ82.5337432
datasetArray
date0.00000000 1662595200
descriptionRNA-A Duplex Naked TIP3P AddedSalt
forceFieldparmBSC0+OL3
ionsModel-
moleculeTypeRna
rev_sequenceGCGUCGCUUCAUGCCAGC
saltConcentration-
sequenceGCUGGCAUGAAGCGACGC
soluteAtoms1156
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1156
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-