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BigNASim
Entry: NAFlex_1j5n_CG
Nucleic Acid Data:
Sequence
CTGAACAATCACCCC
Rev. Sequence
GGGGTGATTGTTCAG
Type
DNA
SubType
B
Chains
duplex
Pdb
-
Ligands
No
Keywords
DNA-B Duplex Naked
MD Simulation >>
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Simulation Metadata
Force Field
parmBSC1
Simulation Date
0.00000000 1720396800
Simulated Time
1,000
Time Step
20 ps
Parts
DNA
Temperature
298K
Water
No
Additional Solvent
No
Counter Ions
No
Ionic Concentration
No
Additional Ions
No
Additional Molecules
No
Ions Parameters
No
Unified Molecular Modeling (UMM) Metadata
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full
UMM)
Simulation Metadata (UMM)
AdditionalIons
No
AdditionalMolecules
No
AdditionalSolvent
No
Author
D.F.
Chains
duplex
Comments
CGeNArate: A Sequence-Dependent Coarse-Grained Model of DNA for Accurate Atomistic MD Simulations of kb-long Duplexes, DOI: 10.1093/nar/gkae444
CounterIons
No
Format
mdcrd
FrameStep
20 ps
Frames
50000
IonicConcentration
No
IonsParameters
No
Ligands
No
NucType
DNA
PDB
NONE
Parts
DNA
RMSd_avg
1.829
RMSd_stdev
0.377
Rgyr_avg
15.941
Rgyr_stdev
0.348
SASA_avg
2666.271
SASA_stdev
15.043
SubType
B
Temperature
298K
Topology
1j5nStripped.pdb
Trajectory
1j5naligned.mdcrd
Water
No
_id
NAFlex_1j5n_CG
dataset
Array
date
0.00000000 1720396800
description
DNA-B Duplex Naked
forceField
CGeNArate
ionsModel
-
moleculeType
Dna
rev_sequence
GGGGTGATTGTTCAG
saltConcentration
-
sequence
CTGAACAATCACCCC
soluteAtoms
30
soluteCharge
-
soluteResidues
30
solventAtoms
-
solventResidues
-
time
1,000
totalAtoms
30
totalCharge
-
totalIons
-
totalResidues
30
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
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