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Entry: NAFlex_colibactin1
Nucleic Acid Data:
Sequence
CGCGAAAATTTTCGCG
Rev. Sequence
|CGCGAAAATTTTCGCG
Type
DNA
SubType
B
Chains
duplex
Pdb
-
Ligands
Colibactin
Keywords
DNA-B Duplex Naked TIP3P Electroneutral
MD Simulation >>
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Simulation Metadata
Force Field
parmBSC1
Simulation Date
0.00000000 1586390400
Simulated Time
400
Time Step
1 ps
Parts
DNA+Colibactin
Temperature
298K
Water
TIP3P
Additional Solvent
No
Counter Ions
K+
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
F.B.
Chains
duplex
Comments
DNA + Colibactin
CounterIons
K+
Format
netcdf
FrameStep
1 ps
Frames
400000
IonicConcentration
Electroneutrality
IonsParameters
Dang
Ligands
Colibactin
NucType
DNA
PDB
NONE
Parts
DNA+Colibactin
RMSd_avg
1.324
RMSd_stdev
0.140
Rgyr_avg
16.534
Rgyr_stdev
0.250
SASA_avg
5759.355
SASA_stdev
93.678
SubType
B
Temperature
298K
Topology
complex_col_nowat.prmtop
Trajectory
complex_col_watmd1_nowat.nc
Water
TIP3P
_id
NAFlex_colibactin1
dataset
Array
date
0.00000000 1586390400
description
DNA-B Duplex Naked TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Dna
rev_sequence
|CGCGAAAATTTTCGCG
saltConcentration
-
sequence
CGCGAAAATTTTCGCG
soluteAtoms
1106
soluteCharge
-30
soluteResidues
33
solventAtoms
-
solventResidues
-
time
400
totalAtoms
1106
totalCharge
-30
totalIons
-
totalResidues
33
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
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