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 | 1586390400000 |
| Simulated Time | 400 |
| 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)
(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 | 1586390400000 |
| 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 |  |
