Entry: NAFlex_ProtDNA_1yo5


Nucleic Sequence:


SequenceACACATCCTGCTA
Rev. SequenceTAGCAGGATGTGT
TypeProt-DNA
SubTypeB
Chainsduplex
Pdb 1YO5
LigandsNo


Force FieldparmBSC1
Simulated Time2,000 ns
Time Step2 ps
PartsDNA
Temperature300K
Water ModelTIP3P
Additional SolventNo
Counter IonsNa+
Ionic ConcentrationElectroneutrality
Additional IonsNo
Additional MoleculesNo
Ions ParametersDang
RMSd2.167 (0.488) Å    
RMSf
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorP.D.
Chainsduplex
CommentsProt-DNA study
CounterIonsNa+
Formatnetcdf
FrameStep2 ps
Frames1000000
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeProt-DNA
PDB1YO5
PartsDNA
RMSd_avg2.167
RMSd_stdev0.488
Rgyr_avg13.963
Rgyr_stdev0.304
SASA_avg4744.842
SASA_stdev79.178
SubTypeB
Temperature300K
Topologytopol.top
Trajectorytraj.nc
WaterTIP3P
_idNAFlex_ProtDNA_1yo5
boxAngle109.471219
boxX65.3586702
boxY65.3586702
boxZ65.3586702
datasetArray
date0.00000000 1453420800
descriptionDNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceFieldparmBSC1
ionsModel-
moleculeTypeProt-Dna
rev_sequenceTAGCAGGATGTGT
saltConcentration-
sequenceACACATCCTGCTA
soluteAtoms824
soluteCharge-24
soluteResidues26
solventAtoms-
solventResidues-
time2,000
totalAtoms824
totalCharge-24
totalIons-
totalResidues26


Selection:
MDAnalysis Atom Selection Syntax
e.g. resid 2:11 or resid 13:20
Frame (start:stop:step)
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Format:        

Analysis

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