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BigNASim
Entry: NAFlex_1zgw_CG
Nucleic Acid Data:
Sequence
GCAAATTAAAGCGCAAGA
Rev. Sequence
TCTTGCGCTTTAATTTGC
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
2.585
RMSd_stdev
0.549
Rgyr_avg
18.606
Rgyr_stdev
0.407
SASA_avg
3186.260
SASA_stdev
17.566
SubType
B
Temperature
298K
Topology
CGTGStripped.pdb
Trajectory
CGTGaligned.mdcrd
Water
No
_id
NAFlex_1zgw_CG
dataset
Array
date
0.00000000 1720396800
description
DNA-B Duplex Naked
forceField
CGeNArate
ionsModel
-
moleculeType
Dna
rev_sequence
TCTTGCGCTTTAATTTGC
saltConcentration
-
sequence
GCAAATTAAAGCGCAAGA
soluteAtoms
36
soluteCharge
-
soluteResidues
36
solventAtoms
-
solventResidues
-
time
1,000
totalAtoms
36
totalCharge
-
totalIons
-
totalResidues
36
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
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