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molecular_mechanics [2013/08/06 16:43] 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 Metal Coordination Spheres ==== | ==== Parameters for Metal Coordination Spheres ==== | ||
- | | [[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?90 |CLICK TO PROCEED TO PARAMETERS}}]] | | + | | [[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}}]] | |