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Entry: NAFlex_ProtDNA_1je8
Nucleic Acid Data:
Sequence
CGTACCCATTAATGGGTACG
Rev. Sequence
CGTACCCATTAATGGGTACG
Type
Prot-DNA
SubType
B
Chains
duplex
Pdb
1JE8
[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
2016-Jan-22
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
Prot-DNA
PDB
1JE8
Parts
DNA
RMSd_avg
2.893
RMSd_stdev
0.690
Rgyr_avg
20.085
Rgyr_stdev
0.413
SASA_avg
7118.152
SASA_stdev
108.327
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_1je8
boxAngle
109.471219
boxX
83.6767384
boxY
83.6767384
boxZ
83.6767384
dataset
Array
date
2016-Jan-22
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Prot-Dna
rev_sequence
CGTACCCATTAATGGGTACG
saltConcentration
-
sequence
CGTACCCATTAATGGGTACG
soluteAtoms
1268
soluteCharge
-38
soluteResidues
40
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
1268
totalCharge
-38
totalIons
-
totalResidues
40
Quality Control
RMSd
2.893 (0.690) Å
Rgyr
20.085 (0.413) Å
SASA
7118.152 (108.327) 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