Entry: NAFlex_2m18


Nucleic Acid Data:


Sequence 1:GGGUUAGGGU
Sequence 2:GGGUUAGGGU
Sequence 3:GGGUUAGGGU
Sequence 4:GGGUUAGGGU
TypeRNA
SubTypeA
Chainsquadruplex
Pdb2M18 [PDB] [NDB]
LigandsNo
KeywordsRNA-A Quadruplex Naked ParmBSC0 TIP3P Electroneutral G-Quadruplex Tetraplex


Simulation Metadata
Force FieldparmBSC1
Simulation Date2014-Mar-03
Simulated Time1,036 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.
Chainsquadruplex
CommentsTERRA
CounterIonsNa+
Formatncdf
FrameStep100ps
Frames10369
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeRNA
PDB2M18
Partsonly RNA
RMSd_avg2.977
RMSd_stdev0.335
Rgyr_avg0.000
Rgyr_stdev0.000
SASA_avg0.000
SASA_stdev0.000
SubTypeA
Temperature300K
Topology2m18.vac.top
Trajectory2m18.dry.nc
WaterTIP3P
_idNAFlex_2m18
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 Quadruplex Naked ParmBSC0 TIP3P Electroneutral G-Quadruplex Tetraplex
forceFieldparmBSC0
ionsModel-
moleculeTypeRna
rev-sequence-
rev_sequenceGGGUUAGGGU
saltConcentration-
sequenceGGGUUAGGGU | GGGUUAGGGU | GGGUUAGGGU | GGGUUAGGGU
sequenceMultiArray
soluteAtoms1304
soluteCharge-36
soluteResidues40
solventAtoms-
solventResidues-
time1,036
totalAtoms1304
totalCharge-36
totalIons-
totalResidues40
Quality Control
RMSd2.977 (0.335) Å    
Rgyr
SASA
RMSf