Entry: NAFlex_2oue


Nucleic Acid Data:


Sequence 1:UCCCXGUCCACCG
Sequence 2:CGGUGAGAAGGG
Sequence 3:GGCAGAGAAACACACGA
TypeRNA
SubTypeA
ChainsdsRNA
Pdb2OUE [PDB] [NDB]
LigandsNo
KeywordsRNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral Flipout-bases Overhanging-bases Hammerhead Ribozyme Bulges


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-24
Simulated Time1,065 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.
ChainsdsRNA
Commentsribozyme
CounterIonsNa+
Formatmdcrd
FrameStep10ps
Frames106515
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeRNA
PDB2OUE
Partsonly RNA
RMSd_avg2.359
RMSd_stdev0.362
Rgyr_avg17.291
Rgyr_stdev0.394
SASA_avg9782.682
SASA_stdev185.829
SubTypeA
Temperature300K
Topology2oue.vac.top
Trajectory2oue.dry.trj.gz
WaterTIP3P
_idNAFlex_2oue
altPDB1X9C 1X9K 1ZFT 1ZFV 1ZFX 2BCY 2BCZ 2D2K 2D2L 2FGP 2NPY 2NPZ 2OUE 2P7D 2P7E 2P7F 3B58 3B5A 3B5F 3B5S 3B91 3BBI 3BBK 3BBM 3CQS 3CR1 3GS1 3GS8 3I2Q 3I2R 3I2S 3I2U 4G6P 4G6R 4G6S
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-24
descriptionRNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral Flipout-bases Overhanging-bases Hammerhead Ribozyme Bulges
forceFieldparmBSC0
ionsModel-
moleculeTypeRna
rev_sequenceUCGUGGUXCAUUACCUGCC
saltConcentration-
sequenceUCCCXGUCCACCG | CGGUGAGAAGGG | GGCAGAGAAACACACGA
sequenceMultiArray
soluteAtoms1968
soluteCharge-56
soluteResidues61
solventAtoms-
solventResidues-
time1,065
totalAtoms1968
totalCharge-56
totalIons-
totalResidues61
Quality Control
RMSd2.359 (0.362) Å    
Rgyr17.291 (0.394) Å    
SASA9782.682 (185.829) Ų    
RMSf