Entry: NAFlex_1hlv


Nucleic Sequence:


SequenceAATCCCGTTTCCAACGAAGGC
Rev. SequenceGCCTTCGTTGGAAACGGGATT
TypeDNA
SubTypeB
Chainsduplex
Pdb 1HLV
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
RMSd2.129 (0.507) 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
PDB1hlv
PartsDNA+protein+ions
RMSd_avg2.129
RMSd_stdev0.507
Rgyr_avg20.924
Rgyr_stdev0.575
SASA_avg7432.181
SASA_stdev187.874
SubTypeB
Temperature298K
Topologyf1hlv_nowat.prmtop
Trajectoryf1hlv_nowat.nc
WaterSPCE
_idNAFlex_1hlv
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
boxX86.2381964
boxY86.2381964
boxZ86.2381964
datasetArray
date0.00000000 1438905600
descriptionDNA-B Duplex Protein-Nuc ParmBSC1 SPC/E AddedSalt
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceGCCTTCGTTGGAAACGGGATT
saltConcentration-
sequenceAATCCCGTTTCCAACGAAGGC
soluteAtoms1331
soluteCharge-40
soluteResidues42
solventAtoms-
solventResidues-
time1,000
totalAtoms1331
totalCharge-40
totalIons-
totalResidues42


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

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