Entry: NAFlex_Subi
Nucleic Sequence:
| Sequence | ATATATATATAT |
| Rev. Sequence | ATATATATATAT |
| Type | DNA |
| SubType | DNA hoogsteen |
| Chains | duplex |
| Pdb | 1GQU |
| Ligands | no |
MD Simulation >> (Click to expand/shrink)
| Force Field | parmBSC1 |
| Simulated Time | 720 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 | 3.776 (1.298) 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/subi12 |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 1ps |
| Frames | 720000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | no |
| NucType | DNA |
| PDB | 1GQU |
| Parts | ions + DNA |
| RMSd_avg | 3.776 |
| RMSd_stdev | 1.298 |
| Rgyr_avg | 13.444 |
| Rgyr_stdev | 0.387 |
| SASA_avg | 4479.243 |
| SASA_stdev | 98.556 |
| SubType | DNA hoogsteen |
| Temperature | 300K |
| Topology | subi12.dry.top |
| Trajectory | subi12.trj.gz |
| Water | TIP3P |
| _id | NAFlex_Subi |
| 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 | 63.7865466 |
| boxY | 63.7865466 |
| boxZ | 63.7865466 |
| dataset | Array |
| date | 0.00000000 1430265600 |
| description | DNA-Hoogsteen Duplex Naked ParmBSC1 TIP3P Electroneutral Flipout-bases Overhanging-bases |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | ATATATATATAT |
| saltConcentration | - |
| sequence | ATATATATATAT |
| soluteAtoms | 766 |
| soluteCharge | -22 |
| soluteResidues | 24 |
| solventAtoms | - |
| solventResidues | - |
| time | 720 |
| totalAtoms | 766 |
| totalCharge | -22 |
| totalIons | - |
| totalResidues | 24 |
