Doubts? Ask BioExcel!
User: Anonymous
myBIGNASim
Register
Login
Logout
Home
Browse
Search
Help
Suppl. Material
Quick Search:
Entry: NAFlex_colibactin1
Nucleic Acid Data:
Sequence
CGCGAAAATTTTCGCG
Rev. Sequence
|CGCGAAAATTTTCGCG
Type
DNA
SubType
B
Chains
duplex
Pdb
-
Ligands
Colibactin
Keywords
DNA-B Duplex Naked TIP3P Electroneutral
MD Simulation >>
(Click to expand/shrink)
Simulation Metadata
Force Field
parmBSC1
Simulation Date
2020-Apr-09
Simulated Time
400 ns
Time Step
1 ps
Parts
DNA+Colibactin
Temperature
298K
Water
TIP3P
Additional Solvent
No
Counter Ions
K+
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
F.B.
Chains
duplex
Comments
DNA + Colibactin
CounterIons
K+
Format
netcdf
FrameStep
1 ps
Frames
400000
IonicConcentration
Electroneutrality
IonsParameters
Dang
Ligands
Colibactin
NucType
DNA
PDB
NONE
Parts
DNA+Colibactin
RMSd_avg
1.324
RMSd_stdev
0.140
Rgyr_avg
16.534
Rgyr_stdev
0.250
SASA_avg
5759.355
SASA_stdev
93.678
SubType
B
Temperature
298K
Topology
complex_col_nowat.prmtop
Trajectory
complex_col_watmd1_nowat.nc
Water
TIP3P
_id
NAFlex_colibactin1
dataset
Array
date
2020-Apr-09
description
DNA-B Duplex Naked TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Dna
rev_sequence
|CGCGAAAATTTTCGCG
saltConcentration
-
sequence
CGCGAAAATTTTCGCG
soluteAtoms
1106
soluteCharge
-30
soluteResidues
33
solventAtoms
-
solventResidues
-
time
400
totalAtoms
1106
totalCharge
-30
totalIons
-
totalResidues
33
Quality Control
RMSd
1.324 (0.140) Å
Rgyr
16.534 (0.250) Å
SASA
5759.355 (93.678) Ų
RMSf
Trajectory Analyses >>
(Click to expand/shrink)
Curves Analysis
Stiffness Analysis
PCAzip Analysis
HBs Analysis
Contacts Analysis