Entry: NAFlex_hybrid


Nucleic Acid Data:


SequenceCTACACGG
Rev. SequenceCCGUGUAG
TypeDNA/RNA
SubTypeA
Chainsduplex
Pdb-
LigandsNo
KeywordsHybrid-A Duplex Naked ParmBSC0 TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-25
Simulated Time1,037 ns
Time Step10 ps
Partsonly nucleic acid
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
CommentsDNA/RNA hybrid
CounterIonsNa+
Formatndcf
FrameStep10 ps
Frames103744
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeDNA/RNA
PDBNONE
Partsonly nucleic acid
RMSd_avg2.750
RMSd_stdev0.431
Rgyr_avg10.355
Rgyr_stdev0.257
SASA_avg3030.588
SASA_stdev49.542
SubTypeA
Temperature300K
Topologyhybrid.vac.top
Trajectoryhybrid.alldry.trj.gz
WaterTIP3P
_idNAFlex_hybrid
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
descriptionHybrid-A Duplex Naked ParmBSC0 TIP3P Electroneutral
forceFieldparmBSC0
ionsModel-
moleculeTypeRna
rev_sequenceCCGUGUAG
saltConcentration-
sequenceCTACACGG
soluteAtoms507
soluteCharge-14
soluteResidues16
solventAtoms-
solventResidues-
time1,037
totalAtoms507
totalCharge-14
totalIons-
totalResidues16
Quality Control
RMSd2.750 (0.431) Å    
Rgyr10.355 (0.257) Å    
SASA3030.588 (49.542) Ų    
RMSf