mm:parameters:iron:cccc
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mm:parameters:iron:cccc [2013/08/05 11:31] ruineves |
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| ====== Iron(III) - CCCC ====== | ====== Iron(III) - CCCC ====== | ||
| + | ### | ||
| + | Rubredoxin is a mononuclear iron tetrahedral metal center coordinated with four cysteines that are not directly connected in the backbone of the protein. | ||
| + | ### | ||
| - | + | | **COORDINATION SPHERE** || | |
| - | + | | {{ :mm:parameters:iron:cccc_non-parameterized.png?120|}} | \\ **Oxidation State:** Fe(III) \\ **Spin Multiplicity:** 6 | | |
| - | | **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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| | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | FE | FE | 55.845 | IMAGE | | + | | FE | FE | 55.845 | {{ :mm:parameters:iron:cccc_parameterized.png?120|}} | |
| | SG | SF | 32.065 | ::: | | | SG | SF | 32.065 | ::: | | ||
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| ==== Bond Parameters ==== | ==== Bond Parameters ==== | ||
| - | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup>** | **l / angstrom** | **REFERENCE** | | + | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>** | **l / Å** | **REFERENCE** | |
| | FE-SF | 80.75 | 2.3170 | [[#references | [Carvalho, 2013]]] | | | FE-SF | 80.75 | 2.3170 | [[#references | [Carvalho, 2013]]] | | ||
| | CT-SF | 237.00 | 1.8100 | | | CT-SF | 237.00 | 1.8100 | | ||
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| ==== Angle Parameters ==== | ==== Angle Parameters ==== | ||
| - | | **Angle** | **K<sub>theta</sub>** / **kcal mol<sup>-1</sup>** | **theta / angstrom** | **REFERENCE** | | + | | **ANGLE** | **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>** | **θ / deg** | **REFERENCE** | |
| | SF-FE-SF | 33.15 | 109.8650 | [[#references | [Carvalho, 2013]]] | | | SF-FE-SF | 33.15 | 109.8650 | [[#references | [Carvalho, 2013]]] | | ||
| | CT-SF-FE | 27.60 | 100.9150 | ::: | | | CT-SF-FE | 27.60 | 100.9150 | ::: | | ||
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| ==== Van der Waals Parameters ==== | ==== Van der Waals Parameters ==== | ||
| - | | **ATOM TYPE** | **R<sub>i</sub> / angstrom** | **epsilon<sub>i</sub> / kcal mol<sup>-1</sup>** | **REFERENCE** | | + | | **ATOM TYPE** | **R<sub>i</sub> / Å** | **ε<sub>i</sub> / kcal mol<sup>-1</sup>** | **REFERENCE** | |
| | FE | 2.6500 | 0.0450 | [[#references | [Giammona, 1984]]] | | | FE | 2.6500 | 0.0450 | [[#references | [Giammona, 1984]]] | | ||
| - | | SF | 2.0000 | 0.2500 | | + | | SF | 2.0000 | 0.2500 | [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 1995]]] | |
| - | ===== Validation of Parameters from MD Simulations ===== | + | ===== Downloads ===== |
| + | |||
| + | | //Parameter File// | {{mm:parameters:iron:cccc-frcmod.zip| .frcmod}} | | ||
| + | | //Coordination Sphere Charges// | {{mm:parameters:iron:cccc_fe-iii.zip| .off}} | | ||
| + | | //Rubredoxin’s PDB File (1IRO.pdb)\ LEAPRC file// | {{mm:parameters:iron:rubredoxin.zip| .pdb, leaprc}} | | ||
| - | ==== Bond Parameters ==== | ||
| - | | **BOND** | **l<sub>0 crystal</sub>** | **l<sub>0 opt</sub>** | **<l><sub>MD</sub> ± sigma(l)** | **<l><sub>MD</sub> ± 2sigma(l)** | | + | ===== References ===== |
| + | ### | ||
| + | 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 | ||
| + | ### | ||
| + | ### | ||
| + | D. A. Giammona, //Ph.D. Thesis//; University of California: Davis, **1984** | ||
| + | ### | ||
mm/parameters/iron/cccc.1375698712.txt.gz · Last modified: 2013/08/05 11:31 by ruineves
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