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BigNASim
Entry: NAFlex_ProtDNA_2kdz
Nucleic Acid Data:
Sequence
AAGATAACGATATTTA
Rev. Sequence
TAAATATCGTTATCTT
Type
Prot-DNA
SubType
B
Chains
duplex
Pdb
2KDZ
[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
Prot-DNA
PDB
2KDZ
Parts
DNA
RMSd_avg
2.455
RMSd_stdev
0.404
Rgyr_avg
16.432
Rgyr_stdev
0.327
SASA_avg
5832.600
SASA_stdev
93.298
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_2kdz
boxAngle
109.471219
boxX
73.2455359
boxY
73.2455359
boxZ
73.2455359
dataset
Array
date
0.00000000 1453420800
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Prot-Dna
rev_sequence
TAAATATCGTTATCTT
saltConcentration
-
sequence
AAGATAACGATATTTA
soluteAtoms
1019
soluteCharge
-30
soluteResidues
32
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
1019
totalCharge
-30
totalIons
-
totalResidues
32
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
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