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Entry: NAFlex_ProtDNA_4f6n
Nucleic Acid Data:
Sequence
CGTATAGACGCGGTGACAC
Rev. Sequence
GTGTCACCGCGTCTATACG
Type
DNA
SubType
B
Chains
duplex
Pdb
4F6N
[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
DNA
PDB
4F6N
Parts
DNA
RMSd_avg
3.087
RMSd_stdev
0.687
Rgyr_avg
19.156
Rgyr_stdev
0.376
SASA_avg
6760.698
SASA_stdev
103.520
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_4f6n
boxAngle
109.471219
boxX
81.1906231
boxY
81.1906231
boxZ
81.1906231
dataset
Array
date
0.00000000 1453420800
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Dna
rev_sequence
GTGTCACCGCGTCTATACG
saltConcentration
-
sequence
CGTATAGACGCGGTGACAC
soluteAtoms
1203
soluteCharge
-36
soluteResidues
38
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
1203
totalCharge
-36
totalIons
-
totalResidues
38
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
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