mm:parameters:iron:ccc_c_2
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| - | ====== Iron(III) - CC[C]2 ====== | ||
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| - | | **Coordination Sphere** | **Oxidation State:** Fe(III) \\ **Spin Multiplicity:** 1 | | ||
| - | | PATH TO IMAGE1 | PATH TO IMAGE2 ((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// | Desulforedoxin | | ||
| - | | //PDB Code// | 1DXG | | ||
| - | | //Crystallographic Resolution// | 1.80 Å | | ||
| - | | //Organism// | Desulfovibrio gigas | | ||
| - | | [[http://www.sciencedirect.com/science/article/pii/S0022283685704652 | [Archer, 1995]]] || | ||
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| - | ===== Parameters Determined ===== | ||
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| - | ==== Atom Types ==== | ||
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| - | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | FE | FE | 55.845 | IMAGE | | ||
| - | | SG | SF | 32.065 | ::: | | ||
| - | | SG | SM | 32.065 | ::: | | ||
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| - | ==== Bond Parameters ==== | ||
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| - | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup>** | **l / angstrom** | **REFERENCE** | | ||
| - | | FE-SF | 84.30 | 2.3100 | [[#references | [Carvalho, 2013]]] | | ||
| - | | FE-SM | 74.1 | 2.3 | ::: | | ||
| - | | CT-SF | 237.00 | 1.8100 | | ||
| - | | SM-CT | 227.00 | 1.8100 | | ||
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| - | ==== Angle Parameters ==== | ||
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| - | | **Angle** | **K<sub>theta</sub>** / **kcal mol<sup>-1</sup>** | **theta / angstrom** | **REFERENCE** | | ||
| - | | SF-FE-SM | 58.4 | 110.0 | [[#references | [Carvalho, 2013]]] | | ||
| - | | FE-SF-CT | 68.5 | 102.0 | ::: | | ||
| - | | FE-SM-CT | 57.3 | 107.0 | ::: | | ||
| - | | SM-FE-SM | 58.4 | 110.0 | ::: | | ||
| - | | SF-FE-SF | 33.2 | 110.0 | ::: | | ||
| - | | SF-CT-H1 | 50.00 | 109.5000 | | ||
| - | | SF-FE-SF | 33.15 | 109.8650 | ::: | | ||
| - | | CT-CT-SF | 50.00 | 108.6000 | | ||
| - | | SM-CT-H1 | 50.00 | 109.5000 | | ||
| - | | CT-SM-CT | 62.00 | 98.9000 | | ||
| - | | CT-CT-SM | 50.00 | 114.7000 | | ||
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| - | ==== Van der Waals Parameters ==== | ||
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| - | | **ATOM TYPE** | **R<sub>i</sub> / angstrom** | **epsilon<sub>i</sub> / kcal mol<sup>-1</sup>** | **REFERENCE** | | ||
| - | | FE | 2.6500 | 0.0450 | [[#references | [Giammona, 1984]]] | | ||
| - | | SF | 2.0000 | 0.2500 | | ||
| - | | SM | 2.0000 | 0.2500 | | ||
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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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| - | A.T.P. Carvalho, A.F.S. Teixeira, MJ.Ramos. [[http://onlinelibrary.wiley.com/doi/10.1002/jcc.23287/abstract;jsessionid=415EECAA000727C4BCBA82544438C428.d03t02 | Parameters for Molecular Dynamics Simulations of Iron-Sulfur Proteins]]. //J. Comput. Chem.//, **2013**, 34, 1540-1548 | ||
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| - | D. A. Giammona, //Ph.D. Thesis//; University of California: Davis, **1984** | ||
mm/parameters/iron/ccc_c_2.1375710786.txt.gz · Last modified: 2013/08/05 14:53 by ruineves
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