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Entry: NAFlex_TF_3v79_11_wholeA
Nucleic Acid Data:
Sequence
GTTACTGTGGXAAAGAAA
Rev. Sequence
TTTCTTTCCCACAGTAAC
Type
Prot+DNA
SubType
B
Chains
duplex
Pdb
-
Ligands
No
Keywords
-B Duplex Naked TIP3P Electroneutral
MD Simulation >>
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Simulation Metadata
Force Field
parmBSC1
Simulation Date
2022-Jul-01
Simulated Time
200 ns
Time Step
2 ps
Parts
Prot+DNA
Temperature
300K
Water
TIP3P
Additional Solvent
No
Counter Ions
K+Cl-
Ionic Concentration
Electroneutrality
Additional Ions
150 mM
Additional Molecules
No
Ions Parameters
Dang
Unified Molecular Modeling (UMM) Metadata
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full
UMM)
Simulation Metadata (UMM)
AdditionalIons
150 mM
AdditionalMolecules
No
AdditionalSolvent
No
Author
M.W.
Chains
duplex
Comments
Milosz MSCA
CounterIons
K+Cl-
Format
xtc
FrameStep
2 ps
Frames
250
IonicConcentration
Electroneutrality
IonsParameters
Dang
Ligands
No
NucType
Prot+DNA
PDB
-
Parts
Prot+DNA
RMSd_avg
3.646
RMSd_stdev
0.430
Rgyr_avg
28.002
Rgyr_stdev
0.716
SASA_avg
28481.505
SASA_stdev
814.113
SubType
B
Temperature
300K
Topology
whole.pdb
Trajectory
whole.xtc
Water
TIP3P
_id
NAFlex_TF_3v79_11_wholeA
dataset
Array
date
2022-Jul-01
description
-B Duplex Naked TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Prot
rev_sequence
TTTCTTTCCCACAGTAAC
saltConcentration
-
sequence
GTTACTGTGGXAAAGAAA
soluteAtoms
8204
soluteCharge
-
soluteResidues
479
solventAtoms
-
solventResidues
-
time
200
totalAtoms
8204
totalCharge
-
totalIons
-
totalResidues
479
Quality Control
RMSd
3.646 (0.430) Å
Rgyr
28.002 (0.716) Å
SASA
28481.505 (814.113) Ų
RMSf
Trajectory Analyses >>
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