Home
News & Events
MuG project
Community
Compute Platform
MuG VRE Compute Platform
Data Manager
Application Offer
Help
Data
BigNASim
Tools
3C Tools Comparison
Flexibility Browser
TADkit 3D genome visualizer
Information Network
Bibliography
Molecular Modeling and Bioinformatics Group
Browse
Home
»
BigNASim
Entry: NAFlex_MuG_TRF1
Nucleic Acid Data:
Sequence
TGTTAGGGTTAGGGTTAG
Rev. Sequence
CTAACCCTAACCCTAACA
Type
Prot-DNA
SubType
B
Chains
duplex
Pdb
1W0T
[PDB]
[NDB]
Ligands
No
Keywords
DNA-B Duplex Complex ParmBSC0 SPC/E
MD Simulation >>
(Click to expand/shrink)
Simulation Metadata
Force Field
parmBSC1
Simulation Date
0.00000000 1462924800
Simulated Time
40
Time Step
1 ps
Parts
DNA+ions
Temperature
300K
Water
SPCE
Additional Solvent
No
Counter Ions
Na+
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
M.P.C.L.
Chains
duplex
Comments
A Comprehensive Model for the Recognition of Human Telomeres by TRF1
CounterIons
Na+
Format
mdcrd
FrameStep
1 ps
Frames
40000
IonicConcentration
0.15M
IonsParameters
Dang
Ligands
No
NucType
Prot-DNA
PDB
1W0T
Parts
DNA+ions
RMSd_avg
2.531
RMSd_stdev
0.433
Rgyr_avg
19.047
Rgyr_stdev
0.396
SASA_avg
6630.185
SASA_stdev
110.995
SubType
B
Temperature
300K
Topology
wtrep1nw.top.gz
Trajectory
rep1nwdt10.trj.gz
Water
SPCE
_id
NAFlex_MuG_TRF1
dataset
Array
date
0.00000000 1462924800
description
DNA-B Duplex Complex ParmBSC0 SPC/E
forceField
parmBSC0
ionsModel
-
moleculeType
Dna
rev_sequence
CTAACCCTAACCCTAACA
saltConcentration
-
sequence
TGTTAGGGTTAGGGTTAG
soluteAtoms
1146
soluteCharge
-35
soluteResidues
36
solventAtoms
-
solventResidues
-
time
40
totalAtoms
1146
totalCharge
-35
totalIons
-
totalResidues
36
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
(Click to expand/shrink)