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Entry: NAFlex_ProtDNA_1j5n
Nucleic Acid Data:
Sequence
CTGAACAATCACCCC
Rev. Sequence
GGGGTGATTGTTCAG
Type
Prot-DNA
SubType
B
Chains
duplex
Pdb
1J5N
[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
1J5N
Parts
DNA
RMSd_avg
1.952
RMSd_stdev
0.423
Rgyr_avg
15.748
Rgyr_stdev
0.320
SASA_avg
5383.606
SASA_stdev
83.367
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_1j5n
boxAngle
109.471219
boxX
70.8669725
boxY
70.8669725
boxZ
70.8669725
dataset
Array
date
2016-Jan-22
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Prot-Dna
rev_sequence
GGGGTGATTGTTCAG
saltConcentration
-
sequence
CTGAACAATCACCCC
soluteAtoms
950
soluteCharge
-28
soluteResidues
30
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
950
totalCharge
-28
totalIons
-
totalResidues
30
Quality Control
RMSd
1.952 (0.423) Å
Rgyr
15.748 (0.320) Å
SASA
5383.606 (83.367) 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