Entry: NAFlex_2hkb


Nucleic Acid Data:


SequenceCTCGGCGCCATC
Rev. SequenceGATGGCGCCGAG
TypeDNA
SubTypeB
Chainsduplex
Pdb2HKB [PDB] [NDB]
Ligandsno
KeywordsDNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-20
Simulated Time590 ns
Time Step1ps
Partsions + DNA
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
AuthorA.P.
Chainsduplex
Comments/gpfs/projects/bsc51/bsc51110/BSC1/300_NMR_DATA/2hkb
CounterIonsNa+
Formatmdcrd
FrameStep1ps
Frames590000
IonicConcentrationElectroneutrality
IonsParametersDang
Ligandsno
NucTypeDNA
PDB2HKB
Partsions + DNA
RMSd_avg2.593
RMSd_stdev0.508
Rgyr_avg13.292
Rgyr_stdev0.287
SASA_avg4330.472
SASA_stdev67.966
SubTypeB
Temperature300K
Topology2hkb.dry.top
Trajectory2hkb_recenter.trj
WaterTIP3P
_idNAFlex_2hkb
altPDB1AX6 2HKB 2HKC 2MAV 2Z2G 2Z2H
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-Apr-20
descriptionDNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceGATGGCGCCGAG
saltConcentration-
sequenceCTCGGCGCCATC
soluteAtoms757
soluteCharge-22
soluteResidues24
solventAtoms-
solventResidues-
time590
totalAtoms757
totalCharge-22
totalIons-
totalResidues24
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-