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Entry: NAFlex_ProtDNA_1c7u
Nucleic Acid Data:
Sequence
CTCGGCTATTAATAGCCGAG
Rev. Sequence
CTCGGCTATTAATAGCCGAG
Type
Prot-DNA
SubType
B
Chains
duplex
Pdb
1C7U
[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
1C7U
Parts
DNA
RMSd_avg
2.709
RMSd_stdev
0.578
Rgyr_avg
20.094
Rgyr_stdev
0.396
SASA_avg
7075.585
SASA_stdev
106.102
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_1c7u
boxAngle
109.471219
boxX
83.6848785
boxY
83.6848785
boxZ
83.6848785
dataset
Array
date
0.00000000 1453420800
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Prot-Dna
rev_sequence
CTCGGCTATTAATAGCCGAG
saltConcentration
-
sequence
CTCGGCTATTAATAGCCGAG
soluteAtoms
1268
soluteCharge
-38
soluteResidues
40
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
1268
totalCharge
-38
totalIons
-
totalResidues
40
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
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