Entry: NAFlex_GAGA_RNA


Nucleic Acid Data:


SequenceCGCGAGAGCG
Rev. Sequence-
TypeRNA
SubTypeA
Chainssingle
Pdb1Q9A [PDB] [NDB]
LigandsNo
KeywordsRNA-A Single Stranded Naked ParmBSC0 TIP3P Electroneutral Sarcin-Ricin Hairpin loop Flipout-bases


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-25
Simulated Time1,022 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.
Chainssingle
CommentsGAGA TL
CounterIonsNa+
Formatmdcrd
FrameStep10ps
Frames102257
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeRNA
PDB1Q9A
Partsonly RNA
RMSd_avg0.874
RMSd_stdev0.200
Rgyr_avg8.245
Rgyr_stdev0.169
SASA_avg1969.080
SASA_stdev36.240
SubTypeA
Temperature300K
Topologygaga.vac.top
Trajectorygaga.alldry.trj.gz
WaterTIP3P
_idNAFlex_GAGA_RNA
altPDB1Q9A 3DVZ 3DW4 3DW5 3DW6 3DW7 480D 483D
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 Single Stranded Naked ParmBSC0 TIP3P Electroneutral Sarcin-Ricin Hairpin loop Flipout-bases
forceFieldparmBSC0
ionsModel-
moleculeTypeRna
rev_sequence-
saltConcentration-
sequenceCGCGAGAGCG
soluteAtoms328
soluteCharge-9
soluteResidues10
solventAtoms-
solventResidues-
time1,022
totalAtoms328
totalCharge-9
totalIons-
totalResidues10
Quality Control
RMSd0.874 (0.200) Å    
Rgyr8.245 (0.169) Å    
SASA1969.080 (36.240) Ų    
RMSf