Entry: NAFlex_v106t9
Nucleic Sequence:
| Sequence | ATCTTTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGAT |
| Rev. Sequence | ATCCTCACCTGCATCCTGAACCCATTGACTCCCAACCCCGTAATAGCGATAGGCCTTGATGTCGATAGCATTGCACGGGTCTTGTTCGATTAACTGCCGCAAAGAT |
| Type | DNA |
| SubType | B |
| Chains | circular duplex |
| Pdb | - |
| Ligands | No |
MD Simulation >> (Click to expand/shrink)
| Force Field | parmBSC1 |
| Simulated Time | 50 ns |
| Time Step | 1ps |
| Parts | DNA |
| Temperature | 300K |
| Water Model | TIP3P |
| Additional Solvent | No |
| Counter Ions | Na+Cl- |
| Ionic Concentration | 0.2M |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | Dang |
| RMSd | 28.746 (7.433) 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.N. |
| Chains | circular duplex |
| Comments | 106bp 9 turns |
| CounterIons | Na+Cl- |
| Format | xtc |
| FrameStep | 1ps |
| Frames | 50000 |
| IonicConcentration | 0.2M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | No |
| Parts | DNA |
| RMSd_avg | 28.746 |
| RMSd_stdev | 7.433 |
| Rgyr_avg | 50.238 |
| Rgyr_stdev | 2.392 |
| SASA_avg | 15997.030 |
| SASA_stdev | 579.811 |
| SubType | B |
| Temperature | 300K |
| Topology | v106t9.gmx.gro |
| Trajectory | v106t9.all.lowres.xtc |
| Water | TIP3P |
| _id | NAFlex_v106t9 |
| 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 1430092800 |
| description | DNA-B Duplex Naked Parm99 TIP3P AddedSalt |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | ATCCTCACCTGCATCCTGAACCCATTGACTCCCAACCCCGTAATAGCGATAGGCCTTGATGTCGATAGCATTGCACGGGTCTTGTTCGATTAACTGCCGCAAAGAT |
| saltConcentration | - |
| sequence | ATCTTTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGAT |
| soluteAtoms | 6731 |
| soluteCharge | 6731 |
| soluteResidues | 212 |
| solventAtoms | - |
| solventResidues | - |
| time | 50 |
| totalAtoms | 6731 |
| totalCharge | 6731 |
| totalIons | - |
| totalResidues | 212 |
