Doubts? Ask BioExcel!
User: Anonymous
myBIGNASim
Register
Login
Logout
Home
Browse
Search
Help
Suppl. Material
Quick Search:
Entry: NAFlex_muAAAT
Nucleic Acid Data:
Sequence
GCATAAATAAATAAATGC
Rev. Sequence
GCATTTATTTATTTATGC
Type
DNA
SubType
B
Chains
duplex
Pdb
-
Ligands
No
Keywords
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt
MD Simulation >>
(Click to expand/shrink)
Simulation Metadata
Force Field
parmBSC0
Simulation Date
2016-May-05
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
(Click to see
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
2.660
RMSd_stdev
0.741
Rgyr_avg
18.260
Rgyr_stdev
0.417
SASA_avg
6530.682
SASA_stdev
124.559
SubType
B
Temperature
298K
Topology
TCGA_nowat.prmtop
Trajectory
TCGA_last250ns.trj
Water
SPCE
_id
NAFlex_muAAAT
boxAngle
109.471219
boxX
80.7856812
boxY
80.7856812
boxZ
80.7856812
dataset
Array
date
2016-May-05
description
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt
forceField
parmBSC0
ionsModel
-
moleculeType
Dna
rev_sequence
GCATTTATTTATTTATGC
saltConcentration
-
sequence
GCATAAATAAATAAATGC
soluteAtoms
1146
soluteCharge
-34
soluteResidues
36
solventAtoms
-
solventResidues
-
time
1,000
totalAtoms
1146
totalCharge
-34
totalIons
-
totalResidues
36
Quality Control
RMSd
2.660 (0.741) Å
Rgyr
18.260 (0.417) Å
SASA
6530.682 (124.559) Ų
RMSf
Trajectory Analyses >>
(Click to expand/shrink)
Curves Analysis
Stiffness Analysis
PCAzip Analysis
NMR_JC Analysis
NMR NOEs Analysis
HBs Analysis
Stacking Analysis
Contacts Analysis