Entry: NAFlex_2oue
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 1429833600000 |
| Simulated Time | 1,065 |
| Time Step | 10ps |
| Parts | only RNA |
| Temperature | 300K |
| Water | TIP3P |
| Additional Solvent | No |
| Counter Ions | Na+ |
| Ionic Concentration | Electroneutrality |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | Dang |
Unified Molecular Modeling (UMM) Metadata
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(Click to see full UMM)
| Simulation Metadata (UMM) | |
|---|---|
| AdditionalIons | No |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | I.F. |
| Chains | dsRNA |
| Comments | ribozyme |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 10ps |
| Frames | 106515 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | No |
| NucType | RNA |
| PDB | 2OUE |
| Parts | only RNA |
| RMSd_avg | 2.359 |
| RMSd_stdev | 0.362 |
| Rgyr_avg | 17.291 |
| Rgyr_stdev | 0.394 |
| SASA_avg | 9782.682 |
| SASA_stdev | 185.829 |
| SubType | A |
| Temperature | 300K |
| Topology | 2oue.vac.top |
| Trajectory | 2oue.dry.trj.gz |
| Water | TIP3P |
| _id | NAFlex_2oue |
| altPDB | 1X9C 1X9K 1ZFT 1ZFV 1ZFX 2BCY 2BCZ 2D2K 2D2L 2FGP 2NPY 2NPZ 2OUE 2P7D 2P7E 2P7F 3B58 3B5A 3B5F 3B5S 3B91 3BBI 3BBK 3BBM 3CQS 3CR1 3GS1 3GS8 3I2Q 3I2R 3I2S 3I2U 4G6P 4G6R 4G6S |
| 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 | 1429833600000 |
| description | RNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral Flipout-bases Overhanging-bases Hammerhead Ribozyme Bulges |
| forceField | parmBSC0 |
| ionsModel | - |
| moleculeType | Rna |
| rev_sequence | UCGUGGUXCAUUACCUGCC |
| saltConcentration | - |
| sequence | UCCCXGUCCACCG | CGGUGAGAAGGG | GGCAGAGAAACACACGA |
| sequenceMulti | Array |
| soluteAtoms | 1968 |
| soluteCharge | -56 |
| soluteResidues | 61 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,065 |
| totalAtoms | 1968 |
| totalCharge | -56 |
| totalIons | - |
| totalResidues | 61 |
| Quality Control | |
|---|---|
| RMSd | 2.359 (0.362) Å  |
| Rgyr | 17.291 (0.394) Å  |
| SASA | 9782.682 (185.829) Ų  |
| RMSf |  |
