Entry: NAFlex_1pqt
Nucleic Sequence:
| Sequence | GCGAAGC |
| Rev. Sequence | - |
| Type | DNA |
| SubType | B-DNA |
| Chains | single hairpin |
| Pdb | 1PQT |
| Ligands | No |
MD Simulation >> (Click to expand/shrink)
| Force Field | parmBSC1 |
| Simulated Time | 1,000 ns |
| Time Step | 200 ps |
| Parts | DNA |
| Temperature | 298K |
| Water Model | TIP3P |
| Additional Solvent | No |
| Counter Ions | Na+Cl- |
| Ionic Concentration | 0.15M |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | Dang |
| RMSd | 0.881 (0.130) Å  |
| RMSf |  |
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
(Click to see full UMM)
| AdditionalIons | No |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | G.P. |
| Chains | single hairpin |
| Comments | - |
| CounterIons | Na+Cl- |
| Format | xtc |
| FrameStep | 200 ps |
| Frames | 5000 |
| IonicConcentration | 0.15M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | 1pqt |
| Parts | DNA |
| RMSd_avg | 0.881 |
| RMSd_stdev | 0.130 |
| Rgyr_avg | 0.000 |
| Rgyr_stdev | 0.000 |
| SASA_avg | 0.000 |
| SASA_stdev | 0.000 |
| SubType | B-DNA |
| Temperature | 298K |
| Topology | init_1pqt.pdb |
| Trajectory | 1pqt_bsc1_5000.xtc |
| Water | TIP3P |
| _id | NAFlex_1pqt |
| altPDB | 1KR8 1PQT 1UB8 |
| 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 1158710400 |
| description | DNA-B Single Stranded Naked ParmBSC1 TIP3P AddedSalt Hairpin |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | - |
| saltConcentration | - |
| sequence | GCGAAGC |
| soluteAtoms | 222 |
| soluteCharge | 222 |
| soluteResidues | 7 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 222 |
| totalCharge | 222 |
| totalIons | - |
| totalResidues | 7 |
