Entry: NAFlex_rna1


Nucleic Acid Data:


SequenceGCCUAUAAACGCCUAUAA
Rev. SequenceUUAUAGGCGUUUAUAGGC
TypeRNA
SubTypeA
Chainsduplex
Pdb-
LigandsNo
KeywordsRNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date2013-Dec-16
Simulated Time200 ns
Time Step10ps
Partsonly RNA
Temperature300K
WaterTIP3P
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
AuthorI.F.
Chainsduplex
CommentsRNA1 from Faustino et al. (2010)
CounterIonsNa+
Formatmdcrd
FrameStep10ps
Frames20001
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeRNA
PDBNONE
Partsonly RNA
RMSd_avg2.515
RMSd_stdev0.595
Rgyr_avg0.000
Rgyr_stdev0.000
SASA_avg0.000
SASA_stdev0.000
SubTypeA
Temperature300K
Topologyrna1.vac.top
Trajectoryrna1.dry.trj.gz
WaterTIP3P
_idNAFlex_rna1
authorsIvan Ivani, Pablo D. Dans, Agnès Noy, Alberto Pérez, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu, Guillem Portella, Federica Battistini, Josep Lluís Gelpí, Carlos González, Michele Vendruscolo, Charles A. Laughton, Sarah A. Harris, David A. Case and Modesto Orozco
datasetArray
date2013-Dec-16
descriptionRNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral
forceFieldparmBSC0
ionsModel-
moleculeTypeRna
rev_sequenceUUAUAGGCGUUUAUAGGC
saltConcentration-
sequenceGCCUAUAAACGCCUAUAA
soluteAtoms1146
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time200
totalAtoms1146
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd2.515 (0.595) Å    
Rgyr
SASA
RMSf