Entry: NAFlex_rna3


Nucleic Acid Data:


SequenceCACGGAACCGGUUCCGUC
Rev. SequenceGACGGAACCGGUUCCGUG
TypeRNA
SubTypeA
Chainsduplex
Pdb-
LigandsNo
KeywordsRNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-25
Simulated Time202 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
CommentsRNA3 from Faustino et al. (2010)
CounterIonsNa+
Formatmdcrd
FrameStep10ps
Frames20285
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeRNA
PDBNONE
Partsonly RNA
RMSd_avg2.633
RMSd_stdev0.621
Rgyr_avg17.138
Rgyr_stdev0.679
SASA_avg6569.346
SASA_stdev100.253
SubTypeA
Temperature300K
Topologyrna3.vac.top
Trajectoryrna3.dry.trj.gz
WaterTIP3P
_idNAFlex_rna3
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_sequenceGACGGAACCGGUUCCGUG
saltConcentration-
sequenceCACGGAACCGGUUCCGUC
soluteAtoms1156
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time202
totalAtoms1156
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd2.633 (0.621) Å    
Rgyr17.138 (0.679) Å    
SASA6569.346 (100.253) Ų    
RMSf