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Entry: NAFlex_ProtDNA_1h9t
Nucleic Acid Data:
Sequence
CATCTGGTACGACCAGATC
Rev. Sequence
GATCTGGTCGTACCAGATG
Type
Prot-DNA
SubType
B
Chains
duplex
Pdb
1H9T
[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
1H9T
Parts
DNA
RMSd_avg
2.423
RMSd_stdev
0.551
Rgyr_avg
19.195
Rgyr_stdev
0.381
SASA_avg
6761.302
SASA_stdev
104.351
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_1h9t
boxAngle
109.471219
boxX
81.1927396
boxY
81.1927396
boxZ
81.1927396
dataset
Array
date
2016-Jan-22
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Prot-Dna
rev_sequence
GATCTGGTCGTACCAGATG
saltConcentration
-
sequence
CATCTGGTACGACCAGATC
soluteAtoms
1204
soluteCharge
-36
soluteResidues
38
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
1204
totalCharge
-36
totalIons
-
totalResidues
38
Quality Control
RMSd
2.423 (0.551) Å
Rgyr
19.195 (0.381) Å
SASA
6761.302 (104.351) 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