Entry: NAFlex_1yo5


Nucleic Sequence:


SequenceACACATCCTGCTA
Rev. SequenceTAGCAGGATGTGT
TypeDNA
SubTypeB
Chainsduplex
Pdb 1YO5
LigandsNo


Force FieldparmBSC1
Simulated Time1,000 ns
Time Step1 ps
PartsDNA+protein+ions
Temperature298K
Water ModelSPCE
Additional SolventNo
Counter IonsK+Cl-
Ionic Concentration0.15M
Additional IonsNo
Additional MoleculesNo
Ions ParametersDang
RMSd2.167 (0.488) Å    
RMSf
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorF.B.
Chainsduplex
Comments-
CounterIonsK+Cl-
Formatnetcdf
FrameStep1 ps
Frames1000000
IonicConcentration0.15M
IonsParametersDang
LigandsNo
NucTypeDNA
PDB1yo5
PartsDNA+protein+ions
RMSd_avg2.167
RMSd_stdev0.488
Rgyr_avg13.963
Rgyr_stdev0.304
SASA_avg4744.831
SASA_stdev79.171
SubTypeB
Temperature298K
Topologyf1yo5_nowat.prmtop
Trajectoryf1yo5_nowat.nc
WaterSPCE
_idNAFlex_1yo5
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
boxAngle109.471219
boxX65.3586702
boxY65.3586702
boxZ65.3586702
datasetArray
date0.00000000 1436832000
descriptionDNA-B Duplex ParmBSC1 SPC/E AddedSalt
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceTAGCAGGATGTGT
saltConcentration-
sequenceACACATCCTGCTA
soluteAtoms824
soluteCharge-24
soluteResidues26
solventAtoms-
solventResidues-
time1,000
totalAtoms824
totalCharge-24
totalIons-
totalResidues26


Selection:
MDAnalysis Atom Selection Syntax
e.g. resid 2:11 or resid 13:20
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Analysis

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