Entry: NAFlex_AAf
Nucleic Acid Data:
| Sequence | CCATACAATACGG |
| Rev. Sequence | CCGTATAGTATGG |
| Type | DNA |
| SubType | B |
| Chains | duplex |
| Pdb | - |
| Ligands | No |
| Keywords | DNA-B Duplex Naked ModifiedNucleotides ParmBSC1 TIP3P Electroneutral |
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2015-Apr-21 |
| Simulated Time | 500 ns |
| Time Step | 1ps |
| Parts | DNA+ions |
| Temperature | 298K |
| 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 | 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 | NONE |
| 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 | 2015-Apr-21 |
| 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 |
| Quality Control | |
|---|---|
| RMSd | 2.596 (0.534) Å  |
| Rgyr | 14.007 (0.318) Å  |
| SASA | 4735.463 (75.954) Ų  |
| RMSf |  |
