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Molecular Modeling and Bioinformatics Group

Entry: NAFlex_RNA_miniABC_KCl_8


Nucleic Acid Data:


SequenceGCGGAGGGCCGGGUGGGC
Rev. SequenceGCCCACCCGGCCCUCCGC
TypeRNA
SubTypeA
Chainsduplex
Pdb-
LigandsNo
KeywordsRNA-A Duplex Naked TIP3P AddedSalt


Simulation Metadata
Force FieldparmBSC1
Simulation Date0.00000000 1662336000
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_avg2.937
RMSd_stdev0.657
Rgyr_avg16.773
Rgyr_stdev0.547
SASA_avg6606.704
SASA_stdev100.081
SubTypeA
Temperature298K
TopologyGCGGAGGGCCGGGUGGGC.dry.parmtop
TrajectoryGCGGAGGGCCGGGUGGGC.dry.5000.nc
WaterTIP3P
_idNAFlex_RNA_miniABC_KCl_8
boxAngle109.471219
boxX82.550182
boxY82.550182
boxZ82.550182
datasetArray
date0.00000000 1662336000
descriptionRNA-A Duplex Naked TIP3P AddedSalt
forceFieldparmBSC0+OL3
ionsModel-
moleculeTypeRna
rev_sequenceGCCCACCCGGCCCUCCGC
saltConcentration-
sequenceGCGGAGGGCCGGGUGGGC
soluteAtoms1164
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1164
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-