Entry: NAFlex_2rn1


Nucleic Acid Data:


SequenceGAGCCCUGGGAGGCUC
Rev. SequenceGCUGGUCCCAGACAGC
TypeRNA
SubTypeA
ChainsssRNA
Pdb2RN1 [PDB] [NDB]
LigandsNo
KeywordsRNA-A Naked ParmBSC0 TIP3P Electroneutral TAR Hairpin-loops Aptamer Kissing-loops


Simulation Metadata
Force FieldparmBSC1
Simulation Date2014-Mar-03
Simulated Time906 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.
ChainsssRNA
Commentskissing loop
CounterIonsNa+
Formatmdcrd
FrameStep10ps
Frames90625
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeRNA
PDB2RN1
Partsonly RNA
RMSd_avg2.063
RMSd_stdev0.324
Rgyr_avg0.000
Rgyr_stdev0.000
SASA_avg0.000
SASA_stdev0.000
SubTypeA
Temperature300K
Topology2rn1.vac.top
Trajectory2rn1.dry.trj.gz
WaterTIP3P
_idNAFlex_2rn1
altPDB1KIS 2RN1
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
date2014-Mar-03
descriptionRNA-A Naked ParmBSC0 TIP3P Electroneutral TAR Hairpin-loops Aptamer Kissing-loops
forceFieldparmBSC0
ionsModel-
moleculeTypeRna
rev_sequenceGCUGGUCCCAGACAGC
saltConcentration-
sequenceGAGCCCUGGGAGGCUC
soluteAtoms1032
soluteCharge-30
soluteResidues32
solventAtoms-
solventResidues-
time906
totalAtoms1032
totalCharge-30
totalIons-
totalResidues32
Quality Control
RMSd2.063 (0.324) Å    
Rgyr
SASA
RMSf