[phenixbb] Duration of a phenix.elbow run

Nigel W Moriarty NWMoriarty at lbl.gov
Wed Jul 1 16:25:48 PDT 2009


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.


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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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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