Entry: NAFlex_1yo5
Nucleic Sequence:
| Sequence | ACACATCCTGCTA |
| Rev. Sequence | TAGCAGGATGTGT |
| Type | DNA |
| SubType | B |
| Chains | duplex |
| Pdb | 1YO5 |
| Ligands | No |
MD Simulation >> (Click to expand/shrink)
| Force Field | parmBSC1 |
| Simulated Time | 1,000 ns |
| Time Step | 1 ps |
| Parts | DNA+protein+ions |
| Temperature | 298K |
| Water Model | SPCE |
| Additional Solvent | No |
| Counter Ions | K+Cl- |
| Ionic Concentration | 0.15M |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | Dang |
| RMSd | 2.167 (0.488) Å  |
| RMSf |  |
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
(Click to see full UMM)
| AdditionalIons | No |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | F.B. |
| Chains | duplex |
| Comments | - |
| CounterIons | K+Cl- |
| Format | netcdf |
| FrameStep | 1 ps |
| Frames | 1000000 |
| IonicConcentration | 0.15M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | 1yo5 |
| Parts | DNA+protein+ions |
| RMSd_avg | 2.167 |
| RMSd_stdev | 0.488 |
| Rgyr_avg | 13.963 |
| Rgyr_stdev | 0.304 |
| SASA_avg | 4744.831 |
| SASA_stdev | 79.171 |
| SubType | B |
| Temperature | 298K |
| Topology | f1yo5_nowat.prmtop |
| Trajectory | f1yo5_nowat.nc |
| Water | SPCE |
| _id | NAFlex_1yo5 |
| 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 |
| boxAngle | 109.471219 |
| boxX | 65.3586702 |
| boxY | 65.3586702 |
| boxZ | 65.3586702 |
| dataset | Array |
| date | 0.00000000 1436832000 |
| description | DNA-B Duplex ParmBSC1 SPC/E AddedSalt |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | TAGCAGGATGTGT |
| saltConcentration | - |
| sequence | ACACATCCTGCTA |
| soluteAtoms | 824 |
| soluteCharge | -24 |
| soluteResidues | 26 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 824 |
| totalCharge | -24 |
| totalIons | - |
| totalResidues | 26 |
