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mm:parameters:iron:cccc [2013/08/05 17:55]
ruineves
mm:parameters:iron:cccc [2013/10/03 18:59] (current)
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  ​+
-|  {{ :​mm:​parameters:​iron:​cccc_non-parameterized.png?​200|}} | 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 ​ |  {{ :​mm:​parameters:​iron:​cccc_parameterized.png?​200|}}  |+|  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]]] ​ |
  
  
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 ===== Downloads ===== ===== Downloads =====
  
-|  //Parameter File// ​ |  {{PATH TO FRCMOD FILE| .frcmod}} ​ | +|  //Parameter File// ​ |  {{mm:​parameters:​iron:​cccc-frcmod.zip| .frcmod}} ​ | 
-|  //​Coordination Sphere Charges// ​ |  {{PATH TO CHARGE FILES| .off}} ​ | +|  //​Coordination Sphere Charges// ​ |  {{mm:​parameters:​iron:​cccc_fe-iii.zip| .off}} ​ | 
-|  //ENZYME’s PDB File (PDB_CODE.pdb)\ LEAPRC file// ​ |  {{PATH TO PDB AND LEAPRC FILES| .pdb, leaprc}} ​ |+|  //Rubredoxin’s PDB File (1IRO.pdb)\ LEAPRC file// ​ |  {{mm:​parameters:​iron:​rubredoxin.zip| .pdb, leaprc}} ​ |
  
  
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 ===== References ===== ===== 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 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** D. A. Giammona, //Ph.D. Thesis//; University of California: Davis, **1984**
 +###
mm/parameters/iron/cccc.1375721738.txt.gz · Last modified: 2013/08/05 17:55 by ruineves