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Molecular Modeling and Bioinformatics Group

Entry: NAFlex_gcf1p_2pro_2dna


Nucleic Acid Data:


Sequence 1:ATAATAAATTATATAATATAATATATATATATATA
Sequence 2:TATATATATATATATTA
TypeProt-DNA
SubTypeB
Chainsduplex
Pdb1PRO [PDB] [NDB]
LigandsNo
Keywords-B Duplex Naked TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date0.00000000 1659312000
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_avg5.948
RMSd_stdev0.866
Rgyr_avg37.516
Rgyr_stdev0.587
SASA_avg43606.923
SASA_stdev1104.158
SubTypeB
Temperature300K
Topology1pro_1longDNA_nowat.prmtop
Trajectory1pro_1longDNA_500reimage.nc
WaterTIP3P
_idNAFlex_gcf1p_2pro_2dna
datasetArray
date0.00000000 1659312000
description-B Duplex Naked TIP3P Electroneutral
forceFieldparmBSC1
ionsModel-
moleculeTypeProt-Dna
rev_sequenceTATTATATAATTTATTAT|ATAATAAATTATATAATATAATATATATATATATA
saltConcentration-
sequenceATAATAAATTATATAATATAATATATATATATATA | TATATATATATATATTA
sequenceMultiArray
soluteAtoms10806
soluteCharge-112
soluteResidues516
solventAtoms-
solventResidues-
time200
totalAtoms10806
totalCharge-112
totalIons-
totalResidues516
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-