<div dir="ltr">Hi Andreas,<div><br></div><div style>My guess is that you have main.simulated_annealing=True also active in your parameter file. You need to set this to False, and then the refinement should proceed.</div><div style>
<br></div><div style>Jeff</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Jun 11, 2013 at 11:44 AM, Andreas Förster <span dir="ltr"><<a href="mailto:docandreas@gmail.com" target="_blank">docandreas@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all,<br>
<br>
I'm trying to get DEN refinement going from the command line. The run aborts quickly with the following error in the log file:<br>
<br>
Sorry: Cartesian simulated annealing should not be turned on for DEN refinement. Annealing settings are controlled in the den parameter scope.<br>
<br>
The DEN scope in input.def looks like this:<br>
<br>
den {<br>
reference_file = den_ref_Jun.pdb<br>
gamma = 0.5<br>
kappa = 0.1<br>
weight = 30<br>
sigma = 0.44<br>
optimize = True<br>
opt_gamma_values = 0 0.2 0.4 0.6 0.8 1<br>
opt_weight_values = 3 10 30 100 300<br>
num_cycles = 12<br>
kappa_burn_in_cycles = 2<br>
bulk_solvent_and_scale = True<br>
refine_adp = True<br>
final_refinement_cycle = False<br>
verbose = False<br>
annealing_type = *torsion cartesian<br>
output_kinemage = False<br>
restraint_network {<br>
lower_distance_cutoff = 3<br>
upper_distance_cutoff = 15<br>
sequence_separation_low = 0<br>
sequence_separation_limit = 10<br>
exclude_hydrogens = True<br>
ndistance_ratio = 1<br>
export_den_pairs = False<br>
den_network_file = None<br>
}<br>
<br>
Annealing type is torsion from what I can tell. What am I doing wrong?<br>
<br>
(Release tag: 1394, Platform: intel-linux-2.6-x86_64 redhat-e6.2)<br>
<br>
<br>
Thanks.<span class="HOEnZb"><font color="#888888"><br>
<br>
<br>
Andreas<br>
<br>
<br>
-- <br>
Andreas Förster, Research Associate<br>
Paul Freemont & Xiaodong Zhang Labs<br>
Department of Biochemistry, Imperial College London<br>
<a href="http://www.msf.bio.ic.ac.uk" target="_blank">http://www.msf.bio.ic.ac.uk</a><br>
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</font></span></blockquote></div><br></div>