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Entry: NAFlex_CTAG_14
Nucleic Acid Data:
Sequence
CGTCTACTAGTGAGGC
Rev. Sequence
GCCTCACTAGTAGACG
Type
DNA
SubType
B
Chains
duplex
Pdb
-
Ligands
No
Keywords
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt
MD Simulation >>
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Simulation Metadata
Force Field
parmBSC1
Simulation Date
2015-May-27
Simulated Time
500 ns
Time Step
1 ps
Parts
DNA+ions
Temperature
298K
Water
TIP3P
Additional Solvent
No
Counter Ions
K+Cl-
Ionic Concentration
0.15M
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
A.B.
Chains
duplex
Comments
-
CounterIons
K+Cl-
Format
netcdf
FrameStep
1 ps
Frames
500000
IonicConcentration
0.15M
IonsParameters
Dang
Ligands
No
NucType
DNA
PDB
NONE
Parts
DNA+ions
RMSd_avg
2.279
RMSd_stdev
0.498
Rgyr_avg
16.597
Rgyr_stdev
0.344
SASA_avg
5709.513
SASA_stdev
87.604
SubType
B
Temperature
298K
Topology
CTAG_14_nowat.top
Trajectory
CTAG_14_nowatReim.nc
Water
TIP3P
_id
NAFlex_CTAG_14
dataset
Array
date
2015-May-27
description
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt
forceField
parmBSC1
ionsModel
-
moleculeType
Dna
rev_sequence
GCCTCACTAGTAGACG
saltConcentration
-
sequence
CGTCTACTAGTGAGGC
soluteAtoms
1013
soluteCharge
-30
soluteResidues
32
solventAtoms
-
solventResidues
-
time
500
totalAtoms
1013
totalCharge
-30
totalIons
-
totalResidues
32
Quality Control
RMSd
2.279 (0.498) Å
Rgyr
16.597 (0.344) Å
SASA
5709.513 (87.604) 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