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molecular_mechanics [2013/08/06 15:53] ruineves |
molecular_mechanics [2013/10/03 19:02] (current) joaocoimbra |
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====== Introduction ====== | ====== Introduction ====== | ||
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The AMBER family of force fields is one of the most commonly used alternatives to describe proteins and drug-like molecules in molecular dynamics simulations. | The AMBER family of force fields is one of the most commonly used alternatives to describe proteins and drug-like molecules in molecular dynamics simulations. | ||
The Data Base presented comprehends sets of parameters developed by the group during round the last ten years. | The Data Base presented comprehends sets of parameters developed by the group during round the last ten years. | ||
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* A first set of parameters accounts for the **systematic parameterization of 12 common lipid types** consistent with the General Amber Force Field (GAFF), with charge-parameters determined with RESP at the HF/6–31G(d) level of theory. | * A first set of parameters accounts for the **systematic parameterization of 12 common lipid types** consistent with the General Amber Force Field (GAFF), with charge-parameters determined with RESP at the HF/6–31G(d) level of theory. | ||
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==== Parameters for Lipids ==== | ==== Parameters for Lipids ==== | ||
- | [[MM:parameters:lipids|{{:mm:parameters:lipids:page_presentation.png?500|CLICK TO PROCEED TO PARAMETERS}}]] | + | [[MM:parameters:lipids|{{:mm:parameters:lipids:page_presentation.png?350|CLICK TO PROCEED TO PARAMETERS}}]] |
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==== Parameters for Metal Coordination Spheres ==== | ==== Parameters for Metal Coordination Spheres ==== | ||
- | | {{ :mm:mn.png?100 |}}|MM:parameters:manganese | FE | CU | ZN | | + | | [[MM:parameters:manganese|{{ :mm:mn.png?100 |CLICK TO PROCEED TO PARAMETERS}}]] | [[MM:parameters:iron|{{ :mm:fe.png?100 |CLICK TO PROCEED TO PARAMETERS}}]] | [[MM:parameters:copper|{{ :mm:cu.png?100 |CLICK TO PROCEED TO PARAMETERS}}]] | [[MM:parameters:zinc|{{ :mm:zn.png?100 |CLICK TO PROCEED TO PARAMETERS}}]] | [[MM:parameters:molybdenum|{{ :mm:mo.png?100 |É PARA O NUNO FAZER}}]] | |
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- | {{ :mm:periodictableofelements.png |SELECT ONE OF THE ELEMENTS FROM THE PERIODIC TABLE TO SHOW THE RESULTS.}} | + | |
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- | [[MM:parameters:manganese]] | + | |
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- | [[MM:parameters:zinc]] | + | |
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- | [[MM:parameters:iron]] | + | |
- | [[MM:parameters:mixed]] |