Entry: NAFlex_AAf
Nucleic Sequence:
| Sequence | CCATACAATACGG |
| Rev. Sequence | CCGTATAGTATGG |
| Type | DNA |
| SubType | B |
| Chains | duplex |
| Pdb | - |
| Ligands | No |
MD Simulation >> (Click to expand/shrink)
| Force Field | parmBSC1 |
| Simulated Time | 500 ns |
| Time Step | 1ps |
| Parts | DNA+ions |
| Temperature | 298K |
| Water Model | TIP3P |
| Additional Solvent | No |
| Counter Ions | Na+ |
| Ionic Concentration | Electroneutrality |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | Dang |
| RMSd | 2.596 (0.534) Å  |
| RMSf |  |
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
(Click to see full UMM)
| AdditionalIons | No |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | P.D. |
| Chains | duplex |
| Comments | only last 250 ns (so 250000 frames out of 500000) |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 1ps |
| Frames | 500000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | No |
| Parts | DNA+ions |
| RMSd_avg | 2.596 |
| RMSd_stdev | 0.534 |
| Rgyr_avg | 14.007 |
| Rgyr_stdev | 0.318 |
| SASA_avg | 4735.463 |
| SASA_stdev | 75.954 |
| SubType | B |
| Temperature | 298K |
| Topology | AAf_nowat.prmtop |
| Trajectory | AAf_last250ns_nowatReimg.mdcrd |
| Water | TIP3P |
| _id | NAFlex_AAf |
| 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 1429574400 |
| description | DNA-B Duplex Naked ModifiedNucleotides ParmBSC1 TIP3P Electroneutral |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | CCGTATAGTATGG |
| saltConcentration | - |
| sequence | CCATACAATACGG |
| soluteAtoms | 824 |
| soluteCharge | -24 |
| soluteResidues | 26 |
| solventAtoms | - |
| solventResidues | - |
| time | 500 |
| totalAtoms | 824 |
| totalCharge | -24 |
| totalIons | - |
| totalResidues | 26 |
