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Entry: NAFlex_ProtDNA_1a0a
Nucleic Acid Data:
Sequence
CTAGTCCCACGTGTGAG
Rev. Sequence
CTCACACGTGGGACTAG
Type
Prot-DNA
SubType
B
Chains
duplex
Pdb
1A0A
[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 1497312000
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
1A0A
Parts
DNA
RMSd_avg
2.400
RMSd_stdev
0.585
Rgyr_avg
17.435
Rgyr_stdev
0.360
SASA_avg
6043.722
SASA_stdev
91.719
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_1a0a
boxAngle
109.471219
boxX
75.3473119
boxY
75.3473119
boxZ
75.3473119
dataset
Array
date
0.00000000 1497312000
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Prot-Dna
rev_sequence
CTCACACGTGGGACTAG
saltConcentration
-
sequence
CTAGTCCCACGTGTGAG
soluteAtoms
1076
soluteCharge
-32
soluteResidues
34
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
1076
totalCharge
-32
totalIons
-
totalResidues
34
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
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