Home
News & Events
MuG project
Community
Compute Platform
MuG VRE Compute Platform
Data Manager
Application Offer
Help
Data
BigNASim
Tools
3C Tools Comparison
Flexibility Browser
TADkit 3D genome visualizer
Information Network
Bibliography
Molecular Modeling and Bioinformatics Group
Browse
Home
»
BigNASim
Entry: NAFlex_ProtDNA_s2lef
Nucleic Acid Data:
Sequence
CACCCTTTGAAGCTC
Rev. Sequence
GAGCTTCAAAGGGTG
Type
DNA
SubType
B
Chains
duplex
Pdb
2LEF
[PDB]
[NDB]
Ligands
No
Keywords
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
MD Simulation >>
(Click to expand/shrink)
Simulation Metadata
Force Field
parmBSC1
Simulation Date
0.00000000 1453507200
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
(Click to see
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
2LEF
Parts
DNA
RMSd_avg
5.319
RMSd_stdev
0.665
Rgyr_avg
15.743
Rgyr_stdev
0.316
SASA_avg
5376.392
SASA_stdev
82.878
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_s2lef
boxAngle
109.471219
boxX
72.0062282
boxY
72.0062282
boxZ
72.0062282
dataset
Array
date
0.00000000 1453507200
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Dna
rev_sequence
GAGCTTCAAAGGGTG
saltConcentration
-
sequence
CACCCTTTGAAGCTC
soluteAtoms
950
soluteCharge
-28
soluteResidues
30
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
950
totalCharge
-28
totalIons
-
totalResidues
30
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
(Click to expand/shrink)