Entry: NAFlex_1d11
Nucleic Sequence:
| Sequence | CGTACG |
| Rev. Sequence | CGTACG |
| Type | DNA |
| SubType | B |
| Chains | duplex |
| Pdb | 1D11 |
| Ligands | No |
MD Simulation >> (Click to expand/shrink)
| Force Field | parmBSC1 |
| Simulated Time | 1,000 ns |
| Time Step | 100ps |
| Parts | only DNA |
| Temperature | 300K |
| Water Model | TIP3P |
| Additional Solvent | No |
| Counter Ions | Na+ |
| Ionic Concentration | Electroneutrality |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | Dang |
| RMSd | 1.765 (0.504) Å  |
| RMSf |  |
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
(Click to see full UMM)
| AdditionalIons | No |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | I.F. |
| Chains | duplex |
| Comments | - |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 100ps |
| Frames | 10001 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | 1d11 |
| Parts | only DNA |
| RMSd_avg | 1.765 |
| RMSd_stdev | 0.504 |
| Rgyr_avg | 9.399 |
| Rgyr_stdev | 0.176 |
| SASA_avg | 2626.773 |
| SASA_stdev | 55.803 |
| SubType | B |
| Temperature | 300K |
| Topology | intercalator.onlydna.top |
| Trajectory | intercalator.onlydna.trj.gz |
| Water | TIP3P |
| _id | NAFlex_1d11 |
| altPDB | 1AO1 1C9Z 1D11 1D14 1D17 1D21 1D22 1D35 1D36 1DL8 1FD5 1FDG 1FN2 1K2J 1K2K 1K2L 1KCI 1M69 1RQY 1UQE 1VTG 1VTW 1XCS 1XCU 1XVR 210D 211D 215D 288D 2D34 2DES 2ET0 2GB9 2GJB 308D 386D 3FX8 3I1D 3NP6 3NX5 452D 465D 4D9X 4D9Y 4GQJ 4MNB |
| authors | Ivan Ivani, Pablo D. Dans, Agnès Noy, Alberto Pérez, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu, Guillem Portella, Federica Battistini, Josep Lluís Gelpí, Carlos González, Michele Vendruscolo, Charles A. Laughton, Sarah A. Harris, David A. Case and Modesto Orozco |
| dataset | Array |
| date | 0.00000000 1429574400 |
| description | DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral Ligand-intercalator |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | CGTACG |
| saltConcentration | - |
| sequence | CGTACG |
| soluteAtoms | 378 |
| soluteCharge | -10 |
| soluteResidues | 12 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 378 |
| totalCharge | -10 |
| totalIons | - |
| totalResidues | 12 |
