Entry: NAFlex_v106Bt10


Nucleic Acid Data:


SequenceTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGATATCTT
Rev. SequenceAAGATATCCTCACCTGCATCCTGAACCCATTGACTCCCAACCCCGTAATAGCGATAGGCCTTGATGTCGATAGCATTGCACGGGTCTTGTTCGATTAACTGCCGCA
TypeDNA
SubTypeB
Chainscircular duplex
Pdb-
LigandsNo
KeywordsDNA-B Duplex Naked Parm99 TIP3P AddedSalt


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-27
Simulated Time100 ns
Time Step1ps
PartsDNA
Temperature300K
WaterTIP3P
Additional SolventNo
Counter IonsNa+Cl-
Ionic Concentration0.2M
Additional IonsNo
Additional MoleculesNo
Ions ParametersDang
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorA.N.
Chainscircular duplex
Comments106bp 10 turns register B
CounterIonsNa+Cl-
Formatxtc
FrameStep1ps
Frames100000
IonicConcentration0.2M
IonsParametersDang
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA
RMSd_avg10.606
RMSd_stdev1.374
Rgyr_avg55.826
Rgyr_stdev0.925
SASA_avg16733.109
SASA_stdev532.780
SubTypeB
Temperature300K
Topologyv106Bt10.gmx.gro
Trajectoryv106Bt10.all.lowres.xtc
WaterTIP3P
_idNAFlex_v106Bt10
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-27
descriptionDNA-B Duplex Naked Parm99 TIP3P AddedSalt
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceAAGATATCCTCACCTGCATCCTGAACCCATTGACTCCCAACCCCGTAATAGCGATAGGCCTTGATGTCGATAGCATTGCACGGGTCTTGTTCGATTAACTGCCGCA
saltConcentration-
sequenceTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGATATCTT
soluteAtoms6731
soluteCharge6731
soluteResidues212
solventAtoms-
solventResidues-
time100
totalAtoms6731
totalCharge6731
totalIons-
totalResidues212
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-