Entry: NAFlex_muCAAT


Nucleic Acid Data:


SequenceGCATCAATCAATCAATGC
Rev. SequenceGCATTGATTGATTGATGC
TypeDNA
SubTypeB
Chainsduplex
Pdb-
LigandsNo
KeywordsDNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt


Simulation Metadata
Force FieldparmBSC1
Simulation Date2016-May-03
Simulated Time1,000 ns
Time Step1 ps
PartsDNA+ions
Temperature298K
WaterSPCE
Additional SolventNo
Counter IonsK+Cl-
Ionic Concentration0.15M
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
CommentsmuABC
CounterIonsK+Cl-
Formatmdcrd
FrameStep1 ps
Frames1000000
IonicConcentration0.15M
IonsParametersDang
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA+ions
RMSd_avg2.391
RMSd_stdev0.530
Rgyr_avg18.352
Rgyr_stdev0.376
SASA_avg6493.919
SASA_stdev102.683
SubTypeB
Temperature298K
TopologyTCGA_nowat.prmtop
TrajectoryTCGA_last250ns.trj
WaterSPCE
_idNAFlex_muCAAT
boxAngle109.471219
boxX80.7086226
boxY80.7086226
boxZ80.7086226
datasetArray
date2016-May-03
descriptionDNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt
forceFieldparmBSC0
ionsModel-
moleculeTypeDna
rev_sequenceGCATTGATTGATTGATGC
saltConcentration-
sequenceGCATCAATCAATCAATGC
soluteAtoms1143
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1143
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd2.391 (0.530) Å    
Rgyr18.352 (0.376) Å    
SASA6493.919 (102.683) Ų    
RMSf