> Mauricio Sica wrote: > > Dear all > > > > I´ve obtained one cluster structure from a protein simulation. Then, as I > > wanted to use this structure as a static model, I checked it with WHAT_IF > > and the result was that as a model is a little poor (a list of bad angles, > > bad distances, problems with planarity and so on as you can imagine). I > > decided to minimize it .So, I performed simulated annealing (300>360>300) > > PRMD (only C_alfas in posre.itp) and then minimization. But the model > > continues didn't improve. I know this would be expected for a "particular" > > conformation at a " particular" moment during the simulation. > > Have any one of you any suggestion? > > > you don't say HOW you got the structure > > g_cluster -method gromos suggests a "real" structure from the trajectory > as best representative for each cluster. > > > I used gromos as well as linkage methods and the results were the same
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