Entry: NAFlex_rna2


Nucleic Acid Data:


SequenceCUAGGUGGAUGACUCAUU
Rev. SequenceAAUGAGUCAUCCACCUAG
TypeRNA
SubTypeA
Chainsduplex
Pdb-
LigandsNo
KeywordsRNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-25
Simulated Time250 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
CommentsRNA2 from Faustino et al. (2010)
CounterIonsNa+
Formatmdcrd
FrameStep10ps
Frames25001
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeRNA
PDBNONE
Partsonly RNA
RMSd_avg2.554
RMSd_stdev0.735
Rgyr_avg16.775
Rgyr_stdev0.581
SASA_avg6518.624
SASA_stdev100.511
SubTypeA
Temperature300K
Topologyrna2.vac.top
Trajectoryrna2.dry.trj.gz
WaterTIP3P
_idNAFlex_rna2
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
date2015-Apr-25
descriptionRNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral
forceFieldparmBSC0
ionsModel-
moleculeTypeRna
rev_sequenceAAUGAGUCAUCCACCUAG
saltConcentration-
sequenceCUAGGUGGAUGACUCAUU
soluteAtoms1148
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time250
totalAtoms1148
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd2.554 (0.735) Å    
Rgyr16.775 (0.581) Å    
SASA6518.624 (100.511) Ų    
RMSf