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Entry: NAFlex_muAGGC
Nucleic Acid Data:
Sequence
GCGCAGGCAGGCAGGCGC
Rev. Sequence
GCGCCTGCCTGCCTGCGC
Type
DNA
SubType
B
Chains
duplex
Pdb
-
Ligands
No
Keywords
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt
MD Simulation >>
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Simulation Metadata
Force Field
parmBSC0
Simulation Date
2016-May-02
Simulated Time
1,000 ns
Time Step
1 ps
Parts
DNA+ions
Temperature
298K
Water
SPCE
Additional Solvent
No
Counter Ions
K+Cl-
Ionic Concentration
0.15M
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
muABC
CounterIons
K+Cl-
Format
mdcrd
FrameStep
1 ps
Frames
1000000
IonicConcentration
0.15M
IonsParameters
Dang
Ligands
No
NucType
DNA
PDB
NONE
Parts
DNA+ions
RMSd_avg
2.819
RMSd_stdev
0.612
Rgyr_avg
18.154
Rgyr_stdev
0.410
SASA_avg
6380.351
SASA_stdev
97.913
SubType
B
Temperature
298K
Topology
TCGA_nowat.prmtop
Trajectory
TCGA_last250ns.trj
Water
SPCE
_id
NAFlex_muAGGC
boxAngle
109.471219
boxX
80.7761607
boxY
80.7761607
boxZ
80.7761607
dataset
Array
date
2016-May-02
description
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt
forceField
parmBSC0
ionsModel
-
moleculeType
Dna
rev_sequence
GCGCCTGCCTGCCTGCGC
saltConcentration
-
sequence
GCGCAGGCAGGCAGGCGC
soluteAtoms
1135
soluteCharge
-34
soluteResidues
36
solventAtoms
-
solventResidues
-
time
1,000
totalAtoms
1135
totalCharge
-34
totalIons
-
totalResidues
36
Quality Control
RMSd
2.819 (0.612) Å
Rgyr
18.154 (0.410) Å
SASA
6380.351 (97.913) 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