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: [email protected] [mailto:phenixbb- [email protected]] 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
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
On 7/1/09 2:43 PM, Dirk wrote: phenix
release (1.3) and the current version (1.4).
Any help would be very appreciated
Thanks
Dirk
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