Entry: NAFlex_1dcw


Nucleic Acid Data:


Sequence 1:CCGGTACCGG
Sequence 2:CCGGTACCGG
Sequence 3:CCGGTACCGG
TypeDNA
SubTypeB
ChainsHolliday Junction
Pdb1DCW [PDB] [NDB]
LigandsNo
KeywordsDNA-B HollidayJunction Naked ParmBSC1 TIP3P Electroneutral 4way-junction inverted-repeat


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-May-05
Simulated Time1,000 ns
Time Step100ps
PartsDNA/DNA+ions
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
AuthorI.F.
ChainsHolliday Junction
Comments-
CounterIonsNa+
Formatmdcrd
FrameStep100ps
Frames10001
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeDNA
PDB1DCW
PartsDNA/DNA+ions
RMSd_avg3.051
RMSd_stdev0.581
Rgyr_avg14.772
Rgyr_stdev0.429
SASA_avg6763.881
SASA_stdev219.414
SubTypeB
Temperature300K
Topologyholliday.vac.top/holliday.helixI.top/holliday.helixII.top
Trajectoryholliday.helixI.trj/holliday.helixII.trj/holliday.helixIions.trj.gz
WaterTIP3P
_idNAFlex_1dcw
altPDB1DCW 1FHZ 1JUC 1L6B 1NT8 1NVN 1ZEZ 3HS1 3IXN 3R86 3U38 3UYA 4M3I 4R48 4R49 4R4A 4R4D
authorsIvan Ivani, Pablo D. Dans, Agnès Noy, Alberto Pérez, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu, Guillem Portella, Federica Battistini, Josep Lluís Gelpí, Carlos González, Michele Vendruscolo, Charles A. Laughton, Sarah A. Harris, David A. Case and Modesto Orozco
datasetArray
date2015-May-05
descriptionDNA-B HollidayJunction Naked ParmBSC1 TIP3P Electroneutral 4way-junction inverted-repeat
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceCCGGTACCGG
saltConcentration-
sequenceCCGGTACCGG | CCGGTACCGG | CCGGTACCGG
sequenceMultiArray
soluteAtoms1260
soluteCharge-36
soluteResidues40
solventAtoms-
solventResidues-
time1,000
totalAtoms1260
totalCharge-36
totalIons-
totalResidues40
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-