Team:EPF-Lausanne/Implementation

From 2009.igem.org

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LOV domains are the light-sensitive portion of phototropins. They absorb light through a flavin cofactor, photo-chemicaly form a covalent bond between the chromophore and a cysteine residue in the protein, and proceed to mediate activation of an attached kinase domain.
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LOV domains are the light-sensitive portion of phototropins. They absorb light through a flavin cofactor, photo-chemicaly form a covalent bond between the chromophore and a cysteine residue in the protein.
===Generating input files===
===Generating input files===
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First we need a compatible .pdb in addition to parameter and topology files. Steps to generate all the input files are explained in detail on this page [[Team:EPF-Lausanne/Modeling/Simulation|How to generate input files]]. This is a kind of summary of the tuto.
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In this section, we explain all the steps to create needed files for namd, except the .conf file.
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We need a compatible .pdb in addition to parameter and topology files to go through. Steps to generate all the input files are explained in detail on this page [[Team:EPF-Lausanne/Modeling/Simulation|How to generate input files]]. This is a kind of summary of the tuto.
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===.conf parameters===
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===Namd .conf parameters===
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We should explain here what are the keywords we use in the .conf.
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Namd can run different kind of simulations, from minimization to MD. Here are the .conf we use. [[Team:EPF-Lausanne/Modeling/NamdConf|NamdConf]]
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===Run a complete simulation===
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===Launch a simulation===
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We start from .pdb, .psf, .rtf generated in the previous section. Complete process is on a separate page [[Team:EPF-Lausanne/Modeling/RunSimulation|How to run a simulation]].
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We start from .pdb, .psf, .rtf generated in the previous section and we explain how to launch namd on both clusters we have access to. Complete process is on a separate page [[Team:EPF-Lausanne/Modeling/RunSimulation|How to launch a simulation]].
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<html>
 
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<title>liste déroulante dynamique</title>
 
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<script language="Javascript" type="text/javascript" >
 
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function choix(formulaire)
 
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{
 
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var j;
 
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var i = formulaire.boite1.selectedIndex;
 
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if (i == 0)
 
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for(j = 1; j <3; j++)
 
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formulaire.boite2.options[j].text="Non!!";
 
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else{
 
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switch (i){
 
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case 1 : var text = new Array( "Marseille","PSG","Monaco");
 
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break;
 
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case 2 : var text = new Array("Toulouse","Agen","Paris");
 
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break;
 
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case 3 : var text = new Array("Dijon","Pau","Gravelines");
 
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break;
 
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}
 
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for(j = 0; j<3; j++)
 
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formulaire.boite2.options[j+1].text=text[j];
 
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formulaire.boite2.selectedIndex=0;
 
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}
 
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</script>
 
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</head>
 
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<body>
 
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<form name="formulaire">
 
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<select name="boite1" onChange="choix(this.form)">
 
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<option selected>...........Choisissez une rubrique...........</option>
 
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<option>foot</option>
 
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<option>rugby</option>
 
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<option>basket</option>
 
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</select>
 
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<select name="boite2">
 
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<option selected>...........Choisissez une rubrique...........</option>
 
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<option></option>
 
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<option></option>
 
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<option></option>
 
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</form>
 
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</select>
 
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</body>
 
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</html>
 
</div><div CLASS="epfl09bouchon"></div>
</div><div CLASS="epfl09bouchon"></div>

Latest revision as of 17:06, 12 August 2009



Contents

Implementation of the simulation


LOV domains are the light-sensitive portion of phototropins. They absorb light through a flavin cofactor, photo-chemicaly form a covalent bond between the chromophore and a cysteine residue in the protein.

Generating input files

In this section, we explain all the steps to create needed files for namd, except the .conf file. We need a compatible .pdb in addition to parameter and topology files to go through. Steps to generate all the input files are explained in detail on this page How to generate input files. This is a kind of summary of the tuto.

Namd .conf parameters

Namd can run different kind of simulations, from minimization to MD. Here are the .conf we use. NamdConf

Launch a simulation

We start from .pdb, .psf, .rtf generated in the previous section and we explain how to launch namd on both clusters we have access to. Complete process is on a separate page How to launch a simulation.


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