[gmx-users] quality of cluster strucutres

[Mauricio Sica]

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?