Entry: NAFlex_2l8f


Nucleic Acid Data:


SequenceGUGAAGCCCGU
Rev. SequenceCGGAGGACACU
TypeRNA
SubTypeA
Chainsduplex
Pdb2L8F [PDB] [NDB]
LigandsNo
KeywordsRNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral Internal-loops


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-May-05
Simulated Time1,750 ns
Time Step100ps
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
Commentsinternal loop
CounterIonsNa+
Formatndcf
FrameStep100ps
Frames17505
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeRNA
PDB2L8F
Partsonly RNA
RMSd_avg1.637
RMSd_stdev0.371
Rgyr_avg12.858
Rgyr_stdev0.327
SASA_avg4124.154
SASA_stdev71.343
SubTypeA
Temperature300K
Topology2l8f.vac.top
Trajectory2l8f.dry.nc
WaterTIP3P
_idNAFlex_2l8f
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-May-05
descriptionRNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral Internal-loops
forceFieldparmBSC0
ionsModel-
moleculeTypeRna
rev_sequenceCGGAGGACACU
saltConcentration-
sequenceGUGAAGCCCGU
soluteAtoms711
soluteCharge-20
soluteResidues22
solventAtoms-
solventResidues-
time1,750
totalAtoms711
totalCharge-20
totalIons-
totalResidues22
Quality Control
RMSd1.637 (0.371) Å    
Rgyr12.858 (0.327) Å    
SASA4124.154 (71.343) Ų    
RMSf