[phenixbb] Duration of a phenix.elbow run

Dirk dirk.reiter at uni-tuebingen.de
Wed Jul 1 14:43:52 PDT 2009


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



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