Entry: NAFlex_56merL_CG


Nucleic Sequence:


SequenceCGCCGGCAGTAGCCGAAAAAATAGGCGCGCGCTCAAAAAAATGCCCCATGCCGCGC
Rev. SequenceGCGCGGCATGGGGCATTTTTTTGAGCGCGCGCCTATTTTTTCGGCTACTGCCGGCG
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
RMSd6.709 (2.305) 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_avg6.709
RMSd_stdev2.305
Rgyr_avg53.791
Rgyr_stdev1.083
SASA_avg9899.217
SASA_stdev48.174
SubTypeB
Temperature298K
Topology56merLStripped.pdb
Trajectory56merLaligned.pdb
WaterNo
_idNAFlex_56merL_CG
datasetArray
date0.00000000 1720137600
descriptionDNA-B Duplex Naked
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceGCGCGGCATGGGGCATTTTTTTGAGCGCGCGCCTATTTTTTCGGCTACTGCCGGCG
saltConcentration-
sequenceCGCCGGCAGTAGCCGAAAAAATAGGCGCGCGCTCAAAAAAATGCCCCATGCCGCGC
soluteAtoms112
soluteCharge-
soluteResidues112
solventAtoms-
solventResidues-
time1,000
totalAtoms112
totalCharge-
totalIons-
totalResidues112


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.