[phenixbb] Duration of a phenix.elbow run

Schubert, Carsten [PRDUS] CSCHUBER at its.jnj.com
Thu Jul 2 06:49:10 PDT 2009


What I do in these cases is a MM minimization of the ligand using a high
quality forcefield and using that output as input into elbow and not
perform an optimization, but have it generate the restraints directly
from the input. The differences between the forcefield and the AM1
calculation in elbow are negligible for protein crystallography
purposes. I would not waste time on o.n. runs. 

HTH

	Carsten

> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
> bounces at phenix-online.org] On Behalf Of Nigel W Moriarty
> Sent: Wednesday, July 01, 2009 7:26 PM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] Duration of a phenix.elbow run
> 
> 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
> Web   : CCI.LBL.gov
> 
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