Entry: NAFlex_ProtDNA_2kdz


Nucleic Acid Data:


SequenceAAGATAACGATATTTA
Rev. SequenceTAAATATCGTTATCTT
TypeProt-DNA
SubTypeB
Chainsduplex
Pdb2KDZ [PDB] [NDB]
LigandsNo
KeywordsDNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date2016-Jan-22
Simulated Time2,000 ns
Time Step2 ps
PartsDNA
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
AuthorP.D.
Chainsduplex
CommentsProt-DNA study
CounterIonsNa+
Formatnetcdf
FrameStep2 ps
Frames1000000
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeProt-DNA
PDB2KDZ
PartsDNA
RMSd_avg2.455
RMSd_stdev0.404
Rgyr_avg16.432
Rgyr_stdev0.327
SASA_avg5832.600
SASA_stdev93.298
SubTypeB
Temperature300K
Topologytopol.top
Trajectorytraj.nc
WaterTIP3P
_idNAFlex_ProtDNA_2kdz
boxAngle109.471219
boxX73.2455359
boxY73.2455359
boxZ73.2455359
datasetArray
date2016-Jan-22
descriptionDNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceFieldparmBSC1
ionsModel-
moleculeTypeProt-Dna
rev_sequenceTAAATATCGTTATCTT
saltConcentration-
sequenceAAGATAACGATATTTA
soluteAtoms1019
soluteCharge-30
soluteResidues32
solventAtoms-
solventResidues-
time2,000
totalAtoms1019
totalCharge-30
totalIons-
totalResidues32
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-