Entry: NAFlex_1vt5
Nucleic Sequence:
| Sequence | CCCCGGGG |
| Rev. Sequence | CCCCGGGG |
| Type | DNA |
| SubType | A |
| Chains | duplex |
| Pdb | 1VT5 |
| Ligands | no |
MD Simulation >> (Click to expand/shrink)
| Force Field | parmBSC1 |
| Simulated Time | 200 ns |
| Time Step | 1ps |
| Parts | ions + 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 | 2.712 (0.457) Å  |
| RMSf |  |
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
(Click to see full UMM)
| AdditionalIons | No |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | A.P. |
| Chains | duplex |
| Comments | /orozco/scratch/parmBSC1/Alberto2/1vt5 |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 1ps |
| Frames | 200000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | no |
| NucType | DNA |
| PDB | 1vt5 |
| Parts | ions + DNA |
| RMSd_avg | 2.712 |
| RMSd_stdev | 0.457 |
| Rgyr_avg | 10.277 |
| Rgyr_stdev | 0.245 |
| SASA_avg | 2968.466 |
| SASA_stdev | 57.231 |
| SubType | A |
| Temperature | 300K |
| Topology | 1vt5.dry.top |
| Trajectory | 1vt5.trj |
| Water | TIP3P |
| _id | NAFlex_1vt5 |
| altPDB | 187D 1RXA 1RXB 1VT5 259D 2A0P |
| 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 1429920000 |
| description | DNA-A Duplex Naked ParmBSC1 TIP3P Electroneutral |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | CCCCGGGG |
| saltConcentration | - |
| sequence | CCCCGGGG |
| soluteAtoms | 502 |
| soluteCharge | -14 |
| soluteResidues | 16 |
| solventAtoms | - |
| solventResidues | - |
| time | 200 |
| totalAtoms | 502 |
| totalCharge | -14 |
| totalIons | - |
| totalResidues | 16 |
