[phenixbb] Duration of a phenix.elbow run
Nigel W Moriarty
NWMoriarty at lbl.gov
Wed Jul 1 16:25:48 PDT 2009
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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>
--
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
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