Dirk That is quite a large molecule but it shouldn't take a few hours. I'm not sure what is happening but I'd guess that a convergence is failing and the upper limit on the number of steps is too great. If I was you, I'd run it overnight and if that fails run it in another quantum package to get the geometry you desire. A different run MAY generate a different starting geometry for the --opt option and that may work better. Each step of the optimisation should take less than 2 minutes. Nigel On 7/1/09 2:43 PM, Dirk wrote:
Hi,
I'm trying to create restraints for a carbohydrate ligand using phenix.elbow. If I run it without the --opt command everything works fine, but I'm not completely happy with the geometry of my ligand after refinement. I tried to get an optimized cif by using --opt command, but the program just runs up to the following output:
MoleculeClass : H:38 C:23 N: 1 O:19 (PDB format) 81 atoms 83 bonds 151 angles 238 dihedrals -------------------- Time Energy delta E RMS Max Step size
and then nothing happens for several hours. Does the optimization needs such a long time and if I let it run overnight (or perhaps longer) I will get an output or is something going wrong? The input is a pdb (I tested several) and I tried both the stable phenix release (1.3) and the current version (1.4).
Any help would be very appreciated
Thanks
Dirk
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