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.
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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