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?
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