[phenixbb] Duration of a phenix.elbow run

[Nigel W Moriarty]

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
>>> phenixbb at phenix-online.org
>>> 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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