Doubts? Ask BioExcel!
User: Anonymous
myBIGNASim
Register
Login
Logout
Home
Browse
Search
Help
Suppl. Material
Quick Search:
Entry: NAFlex_ProtDNA_1iv6
Nucleic Acid Data:
Sequence
CCCTAACCCTAAC
Rev. Sequence
GTTAGGGTTAGGG
Type
Prot-DNA
SubType
B
Chains
duplex
Pdb
1IV6
[PDB]
[NDB]
Ligands
No
Keywords
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
MD Simulation >>
(Click to expand/shrink)
Simulation Metadata
Force Field
parmBSC1
Simulation Date
2016-Jan-22
Simulated Time
2,000 ns
Time Step
2 ps
Parts
DNA
Temperature
300K
Water
TIP3P
Additional Solvent
No
Counter Ions
Na+
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
P.D.
Chains
duplex
Comments
Prot-DNA study
CounterIons
Na+
Format
netcdf
FrameStep
2 ps
Frames
1000000
IonicConcentration
Electroneutrality
IonsParameters
Dang
Ligands
No
NucType
Prot-DNA
PDB
1IV6
Parts
DNA
RMSd_avg
1.842
RMSd_stdev
0.346
Rgyr_avg
14.088
Rgyr_stdev
0.304
SASA_avg
4699.022
SASA_stdev
73.124
SubType
B
Temperature
300K
Topology
topol.top
Trajectory
traj.nc
Water
TIP3P
_id
NAFlex_ProtDNA_1iv6
boxAngle
109.471219
boxX
65.4145724
boxY
65.4145724
boxZ
65.4145724
dataset
Array
date
2016-Jan-22
description
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Prot-Dna
rev_sequence
GTTAGGGTTAGGG
saltConcentration
-
sequence
CCCTAACCCTAAC
soluteAtoms
823
soluteCharge
-24
soluteResidues
26
solventAtoms
-
solventResidues
-
time
2,000
totalAtoms
823
totalCharge
-24
totalIons
-
totalResidues
26
Quality Control
RMSd
1.842 (0.346) Å
Rgyr
14.088 (0.304) Å
SASA
4699.022 (73.124) 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