Entry: NAFlex_CG_5hmC1
Nucleic Acid Data:
| Sequence | XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXGAACGCACGXGCGCGCTGTCXGCCGCGTTTXGACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
| Rev. Sequence | CTGTACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTXGAAACGCGGXGGACAGCGCGXGCGTGCGTTXGAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCC |
| Type | Prot+DNA |
| SubType | B |
| Chains | duplex |
| Pdb | - |
| Ligands | No |
| Keywords | -B Duplex Naked TIP3P Electroneutral |
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2022-Jun-02 |
| 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
(Click to see full UMM)
(Click to see 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 | 3.524 |
| RMSd_stdev | 0.387 |
| Rgyr_avg | 37.205 |
| Rgyr_stdev | 2.340 |
| SASA_avg | 80887.335 |
| SASA_stdev | 5178.423 |
| SubType | B |
| Temperature | 300K |
| Topology | whole.pdb |
| Trajectory | whole.xtc |
| Water | TIP3P |
| _id | NAFlex_CG_5hmC1 |
| dataset | Array |
| date | 2022-Jun-02 |
| description | -B Duplex Naked TIP3P Electroneutral |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | CTGTACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTXGAAACGCGGXGGACAGCGCGXGCGTGCGTTXGAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCC |
| saltConcentration | - |
| sequence | XXXXXXXXGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTXGAACGCACGXGCGCGCTGTCXGCCGCGTTTXGACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC |
| soluteAtoms | 22400 |
| soluteCharge | - |
| soluteResidues | 1098 |
| solventAtoms | - |
| solventResidues | - |
| time | 200 |
| totalAtoms | 22400 |
| totalCharge | - |
| totalIons | - |
| totalResidues | 1098 |
| Quality Control | |
|---|---|
| RMSd | 3.524 (0.387) Å  |
| Rgyr | 37.205 (2.340) Å  |
| SASA | 80887.335 (5178.423) Ų  |
| RMSf |  |