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Molecular Modeling and Bioinformatics Group

Entry: NAFlex_FOXO3_dna_rep5


Nucleic Acid Data:


SequenceGACTATGTAAACAACGC
Rev. SequenceGCGTTGTTTACATAGTC
TypeDNA
SubTypeB
Chainsduplex
Pdb-
LigandsNo
KeywordsDNA-B Duplex Naked SPC/E AddedSalt


Simulation Metadata
Force FieldparmBSC1
Simulation Date0.00000000 1547164800
Simulated Time50
Time Step10 ps
PartsDNA+ions
Temperature300K
WaterSPCE
Additional SolventNo
Counter IonsNa+Cl-
Ionic Concentration0.05M
Additional IonsNo
Additional MoleculesNo
Ions Parameters-
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorA.M.
Chainsduplex
CommentsN/A
CounterIonsNa+Cl-
Formatxtc
FrameStep10 ps
Frames5000
IonicConcentration0.05M
IonsParameters-
LigandsNo
NucTypeDNA
PDB-
PartsDNA+ions
RMSd_avg2.529
RMSd_stdev0.617
Rgyr_avg17.469
Rgyr_stdev0.350
SASA_avg6164.477
SASA_stdev96.579
SubTypeB
Temperature300K
TopologyFOXO3_dna_minim_nowater.gro
TrajectoryFOXO3_dna_rep5_mdprod_sample.xtc
WaterSPCE
_idNAFlex_FOXO3_dna_rep5
datasetArray
date0.00000000 1547164800
descriptionDNA-B Duplex Naked SPC/E AddedSalt
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceGCGTTGTTTACATAGTC
saltConcentration-
sequenceGACTATGTAAACAACGC
soluteAtoms1079
soluteCharge-
soluteResidues34
solventAtoms-
solventResidues-
time50
totalAtoms1079
totalCharge-
totalIons-
totalResidues34
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-