Entry: NAFlex_1kx5
Nucleic Acid Data:
| Sequence | ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT |
| Rev. Sequence | ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT |
| Type | DNA |
| SubType | B |
| Chains | duplex |
| Pdb | 1KX5 [PDB] [NDB] |
| Ligands | No |
| Keywords | DNA-B Duplex Complex ParmBSC1 TIP3P AddedSalt Protein-nuc Nucleosome |
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2015-Apr-25 |
| Simulated Time | 500 ns |
| Time Step | 10 ps |
| Parts | DNA+protein+ions |
| Temperature | 298K |
| Water | TIP3P |
| Additional Solvent | No |
| Counter Ions | Na+ Cl- Mn++ |
| Ionic Concentration | 0.15M |
| 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 | F.B. |
| Chains | duplex |
| Comments | - |
| CounterIons | Na+ Cl- Mn++ |
| Format | mdcrd |
| FrameStep | 10 ps |
| Frames | 50000 |
| IonicConcentration | 0.15M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | 1KX5 |
| Parts | DNA+protein+ions |
| RMSd_avg | 2.432 |
| RMSd_stdev | 0.210 |
| Rgyr_avg | 45.124 |
| Rgyr_stdev | 0.650 |
| SASA_avg | 50308.736 |
| SASA_stdev | 731.131 |
| SubType | B |
| Temperature | 298K |
| Topology | f1kx5_nowat.prmtop |
| Trajectory | f1kx5_1-1000.mdcrd |
| Water | TIP3P |
| _id | NAFlex_1kx5 |
| altPDB | 1KX5 2PYO 3B6F 3B6G 3LJA 3MGP 3MGQ 3MGR 3MGS |
| 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-25 |
| description | DNA-B Duplex Complex ParmBSC1 TIP3P AddedSalt Protein-nuc Nucleosome |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Prot-Dna |
| rev_sequence | ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT |
| saltConcentration | - |
| sequence | ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT |
| soluteAtoms | 21822 |
| soluteCharge | -220 |
| soluteResidues | 1058 |
| solventAtoms | - |
| solventResidues | - |
| time | 500 |
| totalAtoms | 21822 |
| totalCharge | -220 |
| totalIons | - |
| totalResidues | 1058 |
| Quality Control | |
|---|---|
| RMSd | 2.432 (0.210) Å  |
| Rgyr | 45.124 (0.650) Å  |
| SASA | 50308.736 (731.131) Ų  |
| RMSf |  |
