PortoBioComp

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====== Introduction ======

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.

  * 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.

  * The second point of this Data Base is the establishment a **Biomolecular Force Field for Metalloproteins**. Therefore, we present the metallosystems parameterized so far in our group, mainly in the field of **transition metals**. We include bond stretching and angle bending parameters, as well as single point atomic charges for several coordination spheres. All the obtained parameters have been derived using the DFT calculations with the B3LYP hybrid functional.


==== Parameters for Lipids ====

[[MM:parameters:lipids|{{:mm:parameters:lipids:page_presentation.png?350|CLICK TO PROCEED TO PARAMETERS}}]]



==== 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?100 |É PARA O NUNO FAZER}}]]  |
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