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_1a66
Nucleic Acid Data:
Sequence
CAATTTTCCTCG
Rev. Sequence
CGAGGAAAATTG
Type
Prot-DNA
SubType
B
Chains
duplex
Pdb
1A66
[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 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
(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
Prot-DNA
PDB
1A66
Parts
DNA
RMSd_avg
1.792
RMSd_stdev
0.330
Rgyr_avg
13.186
Rgyr_stdev
0.278
SASA_avg
4388.150
SASA_stdev
71.804
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_1a66
boxAngle
109.471219
boxX
62.1142107
boxY
62.1142107
boxZ
62.1142107
dataset
Array
date
0.00000000 1453420800
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Prot-Dna
rev_sequence
CGAGGAAAATTG
saltConcentration
-
sequence
CAATTTTCCTCG
soluteAtoms
761
soluteCharge
-22
soluteResidues
24
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
761
totalCharge
-22
totalIons
-
totalResidues
24
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
(Click to expand/shrink)