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Molecular Modeling and Bioinformatics Group

Entry: NAFlex_FOXA3_mut_rep2


Nucleic Acid Data:


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


Simulation Metadata
Force FieldparmBSC1
Simulation Date0.00000000 1545004800
Simulated Time50
Time Step10 ps
PartsDNA+protein+ions
Temperature300K
WaterSPCE
Additional SolventNo
Counter IonsNa+Cl-
Ionic Concentration0.05M
Additional IonsMg2+
Additional MoleculesNo
Ions Parameters-
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsMg2+
AdditionalMoleculesNo
AdditionalSolventNo
AuthorA.M.
Chainsduplex
CommentsN/A
CounterIonsNa+Cl-
Formatxtc
FrameStep10 ps
Frames5000
IonicConcentration0.05M
IonsParameters-
LigandsNo
NucTypeDNA
PDB-
PartsDNA+protein+ions
RMSd_avg1.843
RMSd_stdev0.224
Rgyr_avg17.244
Rgyr_stdev0.261
SASA_avg11874.403
SASA_stdev242.700
SubTypeB
Temperature300K
TopologyFOXA3_mut_mdeq_rep0_nowater.gro
TrajectoryFOXA3_mut_rep2_mdprod_sample.xtc
WaterSPCE
_idNAFlex_FOXA3_mut_rep2
datasetArray
date0.00000000 1545004800
descriptionDNA-B Duplex Protein-Nuc SPC/E AddedSalt
forceFieldparmBSC1
ionsModel-
moleculeTypeProt
rev_sequenceGCGTTGTTTACATAGTC
saltConcentration-
sequenceGACTATGTAAACAACGC
soluteAtoms2764
soluteCharge-
soluteResidues137
solventAtoms-
solventResidues-
time50
totalAtoms2764
totalCharge-
totalIons-
totalResidues137
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-