Entry: NAFlex_rna3
Nucleic Acid Data:
| Sequence | CACGGAACCGGUUCCGUC |
| Rev. Sequence | GACGGAACCGGUUCCGUG |
| Type | RNA |
| SubType | A |
| Chains | duplex |
| Pdb | - |
| Ligands | No |
| Keywords | RNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral |
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC0 |
| Simulation Date | 2015-Apr-25 |
| Simulated Time | 202 ns |
| 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
(Click to see full UMM)
(Click to see full UMM)
| Simulation Metadata (UMM) | |
|---|---|
| AdditionalIons | No |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | I.F. |
| Chains | duplex |
| Comments | RNA3 from Faustino et al. (2010) |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 10ps |
| Frames | 20285 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | No |
| NucType | RNA |
| PDB | NONE |
| Parts | only RNA |
| RMSd_avg | 2.633 |
| RMSd_stdev | 0.621 |
| Rgyr_avg | 17.138 |
| Rgyr_stdev | 0.679 |
| SASA_avg | 6569.346 |
| SASA_stdev | 100.253 |
| SubType | A |
| Temperature | 300K |
| Topology | rna3.vac.top |
| Trajectory | rna3.dry.trj.gz |
| Water | TIP3P |
| _id | NAFlex_rna3 |
| 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 | 2015-Apr-25 |
| description | RNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral |
| forceField | parmBSC0 |
| ionsModel | - |
| moleculeType | Rna |
| rev_sequence | GACGGAACCGGUUCCGUG |
| saltConcentration | - |
| sequence | CACGGAACCGGUUCCGUC |
| soluteAtoms | 1156 |
| soluteCharge | -34 |
| soluteResidues | 36 |
| solventAtoms | - |
| solventResidues | - |
| time | 202 |
| totalAtoms | 1156 |
| totalCharge | -34 |
| totalIons | - |
| totalResidues | 36 |
| Quality Control | |
|---|---|
| RMSd | 2.633 (0.621) Å  |
| Rgyr | 17.138 (0.679) Å  |
| SASA | 6569.346 (100.253) Ų  |
| RMSf |  |
