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Entry: NAFlex_ProtDNA_1cdw
Nucleic Acid Data:
Sequence
CTGCTATAAAAGGCTG
Rev. Sequence
CAGCCTTTTATAGCAG
Type
Prot-DNA
SubType
B
Chains
duplex
Pdb
1CDW
[PDB]
[NDB]
Ligands
No
Keywords
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
MD Simulation >>
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Simulation Metadata
Force Field
parmBSC1
Simulation Date
2017-Jan-16
Simulated Time
2,000 ns
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
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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
1CDW
Parts
DNA
RMSd_avg
3.232
RMSd_stdev
0.656
Rgyr_avg
16.655
Rgyr_stdev
0.354
SASA_avg
5736.536
SASA_stdev
89.877
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_1cdw
boxAngle
109.471219
boxX
75.6045474
boxY
75.6045474
boxZ
75.6045474
dataset
Array
date
2017-Jan-16
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Prot-Dna
rev_sequence
CAGCCTTTTATAGCAG
saltConcentration
-
sequence
CTGCTATAAAAGGCTG
soluteAtoms
1015
soluteCharge
-30
soluteResidues
32
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
1015
totalCharge
-30
totalIons
-
totalResidues
32
Quality Control
RMSd
3.232 (0.656) Å
Rgyr
16.655 (0.354) Å
SASA
5736.536 (89.877) Ų
RMSf
Trajectory Analyses >>
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Curves Analysis
Stiffness Analysis
PCAzip Analysis
NMR_JC Analysis
NMR NOEs Analysis
HBs Analysis
Stacking Analysis
Contacts Analysis