Entry: NAFlex_1j5n_CG


Nucleic Sequence:


SequenceCTGAACAATCACCCC
Rev. SequenceGGGGTGATTGTTCAG
TypeDNA
SubTypeB
Chainsduplex
Pdb-
LigandsNo


Force FieldparmBSC1
Simulated Time1,000 ns
Time Step20 ps
PartsDNA
Temperature298K
Water ModelNo
Additional SolventNo
Counter IonsNo
Ionic ConcentrationNo
Additional IonsNo
Additional MoleculesNo
Ions ParametersNo
RMSd1.829 (0.377) Å    
RMSf
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorD.F.
Chainsduplex
CommentsCGeNArate: A Sequence-Dependent Coarse-Grained Model of DNA for Accurate Atomistic MD Simulations of kb-long Duplexes, DOI: 10.1093/nar/gkae444
CounterIonsNo
Formatmdcrd
FrameStep20 ps
Frames50000
IonicConcentrationNo
IonsParametersNo
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA
RMSd_avg1.829
RMSd_stdev0.377
Rgyr_avg15.941
Rgyr_stdev0.348
SASA_avg2666.271
SASA_stdev15.043
SubTypeB
Temperature298K
Topology1j5nStripped.pdb
Trajectory1j5naligned.mdcrd
WaterNo
_idNAFlex_1j5n_CG
datasetArray
date0.00000000 1720396800
descriptionDNA-B Duplex Naked
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceGGGGTGATTGTTCAG
saltConcentration-
sequenceCTGAACAATCACCCC
soluteAtoms30
soluteCharge-
soluteResidues30
solventAtoms-
solventResidues-
time1,000
totalAtoms30
totalCharge-
totalIons-
totalResidues30


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

Analyse the selected trajectory using NAFlex server.