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Entry: NAFlex_ProtDNA_3u2b
Nucleic Acid Data:
Sequence
GTCTCTATTGTCCTGG
Rev. Sequence
CCAGGACAATAGAGAC
Type
DNA
SubType
B
Chains
duplex
Pdb
3U2B
[PDB]
[NDB]
Ligands
No
Keywords
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
MD Simulation >>
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Simulation Metadata
Force Field
parmBSC1
Simulation Date
2017-Jan-17
Simulated Time
2,000 ns
Time Step
2 ps
Parts
DNA
Temperature
300K
Water
TIP3P
Additional Solvent
No
Counter Ions
Na+
Ionic Concentration
Electroneutrality
Additional Ions
No
Additional Molecules
No
Ions Parameters
Dang
Unified Molecular Modeling (UMM) Metadata
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full
UMM)
Simulation Metadata (UMM)
AdditionalIons
No
AdditionalMolecules
No
AdditionalSolvent
No
Author
P.D.
Chains
duplex
Comments
Prot-DNA study
CounterIons
Na+
Format
netcdf
FrameStep
2 ps
Frames
1000000
IonicConcentration
Electroneutrality
IonsParameters
Dang
Ligands
No
NucType
DNA
PDB
3U2B
Parts
DNA
RMSd_avg
2.365
RMSd_stdev
0.529
Rgyr_avg
16.632
Rgyr_stdev
0.344
SASA_avg
5733.860
SASA_stdev
88.430
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_3u2b
boxAngle
109.471219
boxX
75.3666429
boxY
75.3666429
boxZ
75.3666429
dataset
Array
date
2017-Jan-17
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Dna
rev_sequence
CCAGGACAATAGAGAC
saltConcentration
-
sequence
GTCTCTATTGTCCTGG
soluteAtoms
1014
soluteCharge
-30
soluteResidues
32
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
1014
totalCharge
-30
totalIons
-
totalResidues
32
Quality Control
RMSd
2.365 (0.529) Å
Rgyr
16.632 (0.344) Å
SASA
5733.860 (88.430) Ų
RMSf
Trajectory Analyses >>
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Curves Analysis
Stiffness Analysis
PCAzip Analysis
NMR_JC Analysis
NMR NOEs Analysis
HBs Analysis
Stacking Analysis
Contacts Analysis