Entry: NAFlex_1dcw
Nucleic Sequence:
| Sequence 1: | CCGGTACCGG |
| Sequence 2: | CCGGTACCGG |
| Sequence 3: | CCGGTACCGG |
| Sequence 4: | CCGGTACCGG |
| Type | DNA |
| SubType | B |
| Chains | Holliday Junction |
| Pdb | 1DCW |
| Ligands | No |
MD Simulation >> (Click to expand/shrink)
| Force Field | parmBSC1 |
| Simulated Time | 1,000 ns |
| Time Step | 100ps |
| Parts | DNA/DNA+ions |
| Temperature | 300K |
| Water Model | TIP3P |
| Additional Solvent | No |
| Counter Ions | Na+ |
| Ionic Concentration | Electroneutrality |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | Dang |
| RMSd | 3.051 (0.581) 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 | Holliday Junction |
| Comments | - |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 100ps |
| Frames | 10001 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | 1dcw |
| Parts | DNA/DNA+ions |
| RMSd_avg | 3.051 |
| RMSd_stdev | 0.581 |
| Rgyr_avg | 14.772 |
| Rgyr_stdev | 0.429 |
| SASA_avg | 6763.881 |
| SASA_stdev | 219.414 |
| SubType | B |
| Temperature | 300K |
| Topology | holliday.vac.top/holliday.helixI.top/holliday.helixII.top |
| Trajectory | holliday.helixI.trj/holliday.helixII.trj/holliday.helixIions.trj.gz |
| Water | TIP3P |
| _id | NAFlex_1dcw |
| altPDB | 1DCW 1FHZ 1JUC 1L6B 1NT8 1NVN 1ZEZ 3HS1 3IXN 3R86 3U38 3UYA 4M3I 4R48 4R49 4R4A 4R4D |
| 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 1430784000 |
| description | DNA-B HollidayJunction Naked ParmBSC1 TIP3P Electroneutral 4way-junction inverted-repeat |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | CCGGTACCGG |
| saltConcentration | - |
| sequence | CCGGTACCGG | CCGGTACCGG | CCGGTACCGG | CCGGTACCGG |
| sequenceMulti | Array |
| soluteAtoms | 1260 |
| soluteCharge | -36 |
| soluteResidues | 40 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 1260 |
| totalCharge | -36 |
| totalIons | - |
| totalResidues | 40 |
