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_1hlv
Nucleic Acid Data:
Sequence
AATCCCGTTTCCAACGAAGGC
Rev. Sequence
GCCTTCGTTGGAAACGGGATT
Type
Prot-DNA
SubType
B
Chains
duplex
Pdb
1HLV
[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
1HLV
Parts
DNA
RMSd_avg
2.582
RMSd_stdev
0.618
Rgyr_avg
21.000
Rgyr_stdev
0.402
SASA_avg
7430.197
SASA_stdev
111.748
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_1hlv
boxAngle
109.471219
boxX
86.2381964
boxY
86.2381964
boxZ
86.2381964
dataset
Array
date
0.00000000 1453420800
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Prot-Dna
rev_sequence
GCCTTCGTTGGAAACGGGATT
saltConcentration
-
sequence
AATCCCGTTTCCAACGAAGGC
soluteAtoms
1331
soluteCharge
-40
soluteResidues
42
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
1331
totalCharge
-40
totalIons
-
totalResidues
42
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
(Click to expand/shrink)