mm:parameters:manganese:ed_py2_wawa_example_page
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| - | ====== Manganese(II) - ED[PY2]WaWa ====== | ||
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| - | | **Coordination Sphere** | **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | | ||
| - | | {{ :mm:parameters:manganese:non-parameterized_edpy2ww_.png?200 |}} | {{ :mm:parameters:manganese:octahedral_highspin_d5.png?400|}} ((The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.)) | | ||
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| - | ---- | ||
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| - | ===== Structure chosen to parameterize ===== | ||
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| - | | **TEST PROTEIN** || | ||
| - | | //Protein// | Pyruvate Kinase | | ||
| - | | //PDB Code// | 2G50 | | ||
| - | | //Crystallographic Resolution// | 1.65 Å | | ||
| - | | //Organism// | Oryctolagus cuniculus | | ||
| - | | [[http://pubs.acs.org/doi/abs/10.1021/bi0524262 | [Williams, 2006]]] || | ||
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| - | ===== Parameters Determined ===== | ||
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| - | ==== Atom Types ==== | ||
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| - | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | MN | M1 | 54.938 | {{ :mm:parameters:manganese:parameterized_edpy2ww_.png?120 |}} | | ||
| - | | OD2 | D1 | 15.9994 | ::: | | ||
| - | | OE1 | E1 | 15.9994 | ::: | | ||
| - | | OW | W1 | 15.9994 | ::: | | ||
| - | | OW | W2 | 15.9994 | ::: | | ||
| - | | HW | HM | 1.00794 | ::: | | ||
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| - | ==== Bond Parameters ==== | ||
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| - | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>** | **l / Å** | **REFERENCE** | | ||
| - | | M1-D1 | 71.90 | 2.0926 | [[#references | [Neves, 2013]]] | | ||
| - | | M1-E1 | 68.77 | 2.1399 | ::: | | ||
| - | | M1-R1 | 55.39 | 2.1382 | ::: | | ||
| - | | M1-R2 | 16.78 | 2.4332 | ::: | | ||
| - | | M1-W1 | 24.75 | 2.3873 | ::: | | ||
| - | | M1-W2 | 50.08 | 2.2004 | ::: | | ||
| - | | D1-C | 656.0 | 1.25 | | ||
| - | | E1-C | 656.0 | 1.25 | | ||
| - | | W1-HM | 553.0 | 0.9572 | | ||
| - | | W2-HM | 553.0 | 0.9572 | | ||
| - | | c-R2 | 648.0 | 1.214 | | ||
| - | | c-R1 | 648.0 | 1.214 | | ||
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| - | ==== Angle Parameters ==== | ||
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| - | | **ANGLE** | **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>** | **θ / deg** | **REFERENCE** | | ||
| - | | D1-M1-E1 | 38.27 | 96.6209 | [[#references | [Neves, 2013]]] | | ||
| - | | D1-M1-R1 | 23.41 | 104.8054 | ::: | | ||
| - | | D1-M1-R2 | 12.445 | 169.3708 | ::: | | ||
| - | | D1-M1-W1 | 69.3 | 72.8299 | ::: | | ||
| - | | D1-M1-W2 | 26.19 | 103.5245 | ::: | | ||
| - | | E1-M1-R1 | 29.696 | 97.7449 | ::: | | ||
| - | | E1-M1-R2 | 13.94 | 93.9317 | ::: | | ||
| - | | E1-M1-W1 | 25.05 | 168.0717 | ::: | | ||
| - | | E1-M1-W2 | 52.2 | 89.0644 | ::: | | ||
| - | | R1-M1-R2 | 128.3 | 80.3387 | ::: | | ||
| - | | R1-M1-W1 | 20.47 | 80.0896 | ::: | | ||
| - | | R1-M1-W2 | 18.05 | 149.8517 | ::: | | ||
| - | | R2-M1-W1 | 13.736 | 96.5418 | ::: | | ||
| - | | R2-M1-W2 | 27.09 | 77.9339 | ::: | | ||
| - | | W1-M1-W2 | 15.008 | 98.6963 | ::: | | ||
| - | | M1-D1-C | 14.829 | 125.0463 | ::: | | ||
| - | | M1-E1-C | 42.056 | 122.8295 | ::: | | ||
| - | | M1-R1-c | 47.47 | 122.0775 | ::: | | ||
| - | | M1-R2-c | 57.66 | 110.2798 | ::: | | ||
| - | | M1-W1-HM | 12.10 | 86.3993 | ::: | | ||
| - | | M1-W2-HM | 28.96 | 88.1336 | ::: | | ||
| - | | HM-W1-HM | 100.0 | 104.52 | | ||
| - | | HM-W2-HM | 100.0 | 104.52 | | ||
| - | | HM-W3-HM | 100.0 | 104.52 | | ||
| - | | D1-C-CT | 70.0 | 117.0 | | ||
| - | | D1-C-O2 | 80.0 | 126.0 | | ||
| - | | E1-C-CT | 70.0 | 117.0 | | ||
| - | | E1-C-O2 | 80.0 | 126.0 | | ||
| - | | c3-c-R2 | 68.0 | 123.11 | | ||
| - | | R1-c-c | 66.8 | 122.34 | | ||
| - | | o-c-R1 | 79.1 | 127.33 | | ||
| - | | c-c-R2 | 66.8 | 122.34 | | ||
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| - | ==== Van der Waals Parameters ==== | ||
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| - | | **ATOM TYPE** | **R<sub>i</sub> / Å** | **ε<sub>i</sub> / kcal mol<sup>-1</sup>** | **REFERENCE** | | ||
| - | | M1 | 1.4544 | 0.03 | [[http://pubs.acs.org/doi/abs/10.1021/jp054177x | [Babu, 2006]]] | | ||
| - | | D1 | 1.6612 | 0.21 | | ||
| - | | E1 | 1.6612 | 0.21 | | ||
| - | | R1 | 1.6612 | 0.2100 | | ||
| - | | R2 | 1.6612 | 0.2100 | | ||
| - | | W1 | 1.7683 | 0.152 | | ||
| - | | W2 | 1.7683 | 0.152 | | ||
| - | | HM | 0.6000 | 0.0157 | [[LINK | [Cornel, 1995]]] | | ||
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| - | ===== Validation of Parameters from MD Simulations ===== | ||
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| - | ==== Bond Parameters ==== | ||
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| - | | **BOND** | **l<sub>0 crystal</sub>** | **l<sub>0 opt</sub>** | **‹l›<sub>MD</sub> ± σ(l)** | **‹l›<sub>MD</sub> ± 2σ(l)** | | ||
| - | | M1-D1 | 1.97 | 2.09 | 2.16 ± 0.06 | [2.095; 2.225] | | ||
| - | | M1-E1 | 1.96 | 2.14 | 2.22 ± 0.06 | [2.153; 2.281] | | ||
| - | | M1-R1 | 1.98 | 2.14 | 2.13 ± 0.07 | [2.059; 2.192] | | ||
| - | | M1-R2 | 1.95 | 2.43 | 2.4 ± 0.1 | [2.276; 2.473] | | ||
| - | | M1-W1 | 2.29 | 2.39 | 2.4 ± 0.1 | [2.289; 2.537] | | ||
| - | | M1-W2 | 2.26 | 2.20 | 2.18 ± 0.08 | [2.100; 2.258] | | ||
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| - | ==== Angle Parameters ==== | ||
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| - | | **ANGLE** | **θ<sub>0 crystal</sub>** | **θ<sub>0 QM</sub>** | **‹θ›<sub>MD</sub> ± σ(θ)** | **‹θ›<sub>MD</sub> ± 2σ(θ)** | | ||
| - | | D1-M1-E1 | 97.0 | 96.6 | 99 ± 5 | [89.0; 108.1] | | ||
| - | | D1-M1-R1 | 90.8 | 104.8 | 103 ± 5 | [93.1; 112.4] | | ||
| - | | D1-M1-R2 | 153.6 | 169.4 | 170 ± 5 | [159.4; 180.1] | | ||
| - | | D1-M1-W1 | 78.1 | 72.8 | 75 ± 4 | [67.8; 82.2] | | ||
| - | | D1-M1-W2 | 113.2 | 103.5 | 110 ± 5 | [99.5; 120.6] | | ||
| - | | E1-M1-R1 | 91.7 | 97.7 | 101 ± 5 | [91.1; 110.3] | | ||
| - | | E1-M1-R2 | 105.0 | 93.9 | 75 ± 5 | [64.3; 86.1] | | ||
| - | | E1-M1-W1 | 163.9 | 168.1 | 168 ± 4 | [159.5; 176.5] | | ||
| - | | E1-M1-W2 | 84.8 | 89.1 | 80 ± 4 | [71.4; 87.7] | | ||
| - | | R1-M1-R2 | 74.4 | 80.3 | 75 ± 2 | [70.9; 79.1] | | ||
| - | | R1-M1-W1 | 103.6 | 80.1 | 79 ± 7 | [63.7; 93.7] | | ||
| - | | R1-M1-W2 | 156.0 | 149.9 | 146 ± 5 | [136.7; 155.4] | | ||
| - | | R2-M1-W1 | 84.2 | 96.5 | 111 ± 7 | [97.0; 124.2] | | ||
| - | | R2-M1-W2 | 83.5 | 77.9 | 73 ± 5 | [63.3; 82.5] | | ||
| - | | W1-M1-W2 | 83.1 | 98.7 | 105 ± 10 | [85.6; 123.9] | | ||
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| - | ===== Downloads ===== | ||
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| - | | //Parameter File// | {{PATH TO FRCMOD FILE| .frcmod}} | | ||
| - | | //Coordination Sphere Charges// | {{PATH TO CHARGE FILES| .off}} | | ||
| - | | //ENZYME’s PDB File (PDB_CODE.pdb)\ LEAPRC file// | {{PATH TO PDB AND LEAPRC FILES| .pdb, leaprc}} | | ||
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| - | ===== References ===== | ||
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| - | Neves, R.P.P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. [[http://pubs.acs.org/doi/abs/10.1021/ct400055v | Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins]] . //J. Chem. Theory Comput.//, **2013**, 9 (6), 2718–2732 | ||
mm/parameters/manganese/ed_py2_wawa_example_page.1374846678.txt.gz · Last modified: 2013/07/26 14:51 by ruineves
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