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Molecular Modeling and Bioinformatics Group

Entry: NAFlex_FOXO3_crystal_rep2


Nucleic Acid Data:


SequenceGACTATGTAAACAACGC
Rev. SequenceGCGTTGTTTACATAGTC
TypeDNA
SubTypeB
Chainsduplex
Pdb2UZK [PDB] [NDB]
LigandsNo
KeywordsDNA-B Duplex Protein-Nuc SPC/E AddedSalt


Simulation Metadata
Force FieldparmBSC1
Simulation Date0.00000000 1545264000
Simulated Time50
Time Step10 ps
PartsDNA+protein+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
PDB2UZK
PartsDNA+protein+ions
RMSd_avg79.254
RMSd_stdev23.346
Rgyr_avg80.353
Rgyr_stdev21.012
SASA_avg11740.935
SASA_stdev669.028
SubTypeB
Temperature300K
TopologyFOXO3_orig_minim_nowater.gro
TrajectoryFOXO3_rep2_mdprod_sample.xtc
WaterSPCE
_idNAFlex_FOXO3_crystal_rep2
datasetArray
date0.00000000 1545264000
descriptionDNA-B Duplex Protein-Nuc SPC/E AddedSalt
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceGCGTTGTTTACATAGTC
saltConcentration-
sequenceGACTATGTAAACAACGC
soluteAtoms2620
soluteCharge-
soluteResidues131
solventAtoms-
solventResidues-
time50
totalAtoms2620
totalCharge-
totalIons-
totalResidues131
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-