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Molecular Modeling and Bioinformatics Group

Entry: NAFlex_gcf1p_4pro_4dna


Nucleic Acid Data:


Sequence 1:TATATTATATAATTTATTAT
Sequence 2:ATAATAAATTATATAATATA
Sequence 3:TATATTATATAATTTATTAT
Sequence 4:ATAATAAATT
TypeProt-DNA
SubTypeB
Chainsduplex
Pdb1PRO [PDB] [NDB]
LigandsNo
Keywords-B Duplex Naked TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date0.00000000 1659398400
Simulated Time200
Time Step1 ps
PartsProt,DNA
Temperature300K
WaterTIP3P
Additional SolventNo
Counter IonsK+,Cl-
Ionic ConcentrationElectroneutrality
Additional IonsNo
Additional MoleculesNo
Ions ParametersDang
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorF.B.
Chainsduplex
Commentsgcf1p project
CounterIonsK+,Cl-
Formatnetcdf
FrameStep1 ps
Frames48000
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeProt-DNA
PDB1PRO
PartsProt,DNA
RMSd_avg5.257
RMSd_stdev0.814
Rgyr_avg47.093
Rgyr_stdev0.701
SASA_avg65665.630
SASA_stdev1271.224
SubTypeB
Temperature300K
Topology1pro_1longDNA_nowat.prmtop
Trajectory1pro_1longDNA_500reimage.nc
WaterTIP3P
_idNAFlex_gcf1p_4pro_4dna
datasetArray
date0.00000000 1659398400
description-B Duplex Naked TIP3P Electroneutral
forceFieldparmBSC1
ionsModel-
moleculeTypeProt-Dna
rev_sequenceATATAATATA|TATATTATATAATTTATTAT|ATAATAAATTATATAATATA|TATATTATATAATTTATTAT
saltConcentration-
sequenceTATATTATATAATTTATTAT | ATAATAAATTATATAATATA | TATATTATATAATTTATTAT | ATAATAAATT
sequenceMultiArray
soluteAtoms17686
soluteCharge-96
soluteResidues904
solventAtoms-
solventResidues-
time200
totalAtoms17686
totalCharge-96
totalIons-
totalResidues904
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-