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Entry: NAFlex_ProtDNA_2stw
Nucleic Acid Data:
Sequence
TCGAACTTCCGGCTCGA
Rev. Sequence
TCGAGCCGGAAGTTCGA
Type
DNA
SubType
B
Chains
duplex
Pdb
2STW
[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
0.00000000 1453420800
Simulated Time
2,000
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
2STW
Parts
DNA
RMSd_avg
2.137
RMSd_stdev
0.382
Rgyr_avg
17.533
Rgyr_stdev
0.360
SASA_avg
6039.114
SASA_stdev
95.162
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_2stw
boxAngle
109.471219
boxX
75.4204603
boxY
75.4204603
boxZ
75.4204603
dataset
Array
date
0.00000000 1453420800
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Dna
rev_sequence
TCGAGCCGGAAGTTCGA
saltConcentration
-
sequence
TCGAACTTCCGGCTCGA
soluteAtoms
1076
soluteCharge
-32
soluteResidues
34
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
1076
totalCharge
-32
totalIons
-
totalResidues
34
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
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