Entry: NAFlex_v106t9
Nucleic Acid Data:
| Sequence | ATCTTTGCGGCAGTTAATCGAACAAGACCCGTGCAATGCTATCGACATCAAGGCCTATCGCTATTACGGGGTTGGGAGTCAATGGGTTCAGGATGCAGGTGAGGAT |
| Rev. Sequence | ATCCTCACCTGCATCCTGAACCCATTGACTCCCAACCCCGTAATAGCGATAGGCCTTGATGTCGATAGCATTGCACGGGTCTTGTTCGATTAACTGCCGCAAAGAT |
| Type | DNA |
| SubType | B |
| Chains | circular duplex |
| Pdb | - |
| Ligands | No |
| Keywords | DNA-B Duplex Naked Parm99 TIP3P AddedSalt |
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2015-Apr-27 |
| Simulated Time | 50 ns |
| Time Step | 1ps |
| Parts | DNA |
| Temperature | 300K |
| Water | TIP3P |
| Additional Solvent | No |
| Counter Ions | Na+Cl- |
| Ionic Concentration | 0.2M |
| 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 | 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 | NONE |
| 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 | 2015-Apr-27 |
| 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 |
| Quality Control | |
|---|---|
| RMSd | 28.746 (7.433) Å  |
| Rgyr | 50.238 (2.392) Å  |
| SASA | 15997.030 (579.811) Ų  |
| RMSf |  |
