Entry: NAFlex_ProtDNA_2hdc


Nucleic Acid Data:


SequenceGCTTAAAATAACAATAC
Rev. SequenceGTATTGTTATTTTAAGC
TypeProt-DNA
SubTypeB
Chainsduplex
Pdb2HDC [PDB] [NDB]
LigandsNo
KeywordsDNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date2016-Jan-22
Simulated Time2,000 ns
Time Step2 ps
PartsDNA
Temperature300K
WaterTIP3P
Additional SolventNo
Counter IonsNa+
Ionic ConcentrationElectroneutrality
Additional IonsNo
Additional MoleculesNo
Ions ParametersDang
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorP.D.
Chainsduplex
CommentsProt-DNA study
CounterIonsNa+
Formatnetcdf
FrameStep2 ps
Frames1000000
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeProt-DNA
PDB2HDC
PartsDNA
RMSd_avg2.451
RMSd_stdev0.570
Rgyr_avg17.463
Rgyr_stdev0.342
SASA_avg6133.179
SASA_stdev93.834
SubTypeB
Temperature300K
Topologytopol.top
Trajectorytraj.nc
WaterTIP3P
_idNAFlex_ProtDNA_2hdc
boxAngle109.471219
boxX75.2935821
boxY75.2935821
boxZ75.2935821
datasetArray
date2016-Jan-22
descriptionDNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceFieldparmBSC1
ionsModel-
moleculeTypeProt-Dna
rev_sequenceGTATTGTTATTTTAAGC
saltConcentration-
sequenceGCTTAAAATAACAATAC
soluteAtoms1082
soluteCharge-32
soluteResidues34
solventAtoms-
solventResidues-
time2,000
totalAtoms1082
totalCharge-32
totalIons-
totalResidues34
Quality Control
RMSd2.451 (0.570) Å    
Rgyr17.463 (0.342) Å    
SASA6133.179 (93.834) Ų    
RMSf