[phenixbb] Duration of a phenix.elbow run
Nigel W Moriarty
NWMoriarty at lbl.gov
Mon Jul 6 09:31:06 PDT 2009
Dirk
Lets talk off-line. Can you send me the input that you send to eLBOW?
You do need to have GAMESS installed and then you need to do a small bit
of scripting by changing the GAMESS.csh file. I can help with that.
Nigel
On 7/3/09 5:27 PM, Dirk wrote:
> Hi,
>
> thanks for the suggestions I tried to run it overnight, but without any
> result. I also tried to use GAMESS, but even so the GAMESS run is
> started I still get the message "GAMESS doesn't seem to be installed"
> and "mv: Aufruf von stat für „elbow.drgfin_pdb.012.gamess.gam“ nicht
> möglich: No such file or directory" even so the file exists. Since I'm
> not experienced in python I wasn't able to find the reason for that by
> inspecting the GAMESSMixins.py script.
> I would like to try the forcefield approach, but don't know if there is
> any freeware available for that purpose - I would be glad about
> suggestions .
> For the moment I "solved" the problem by manually editing the cif file
> using values from the refmac monomer and link libraries for the
> restraints. I still would be really interested in getting elbow to work
> to get better restraints for this ligand and to avoid the time consuming
> manual creation of cif files in the future.
>
> Thank you again for the replies
>
> Dirk
>
>
> Schubert, Carsten [PRDUS] schrieb:
>
>> 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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>>>> phenixbb at phenix-online.org
>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>
>>>>
>>>>
>>>>
>>> --
>>> 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
>>>
>>> _______________________________________________
>>> phenixbb mailing list
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>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
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>
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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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