[phenixbb] elbow

Mengbin Chen mengbinc at sas.upenn.edu
Thu Jun 13 11:53:40 PDT 2013


Dear Dr. Dias,

I tried the command line in Terminal, but Elbow still regularized the
conformation and bonds of the ligand and the result turned out to be the
same with that I ran thorough GUI. The thing is that the input pdb file has
a conformation the ligand should adopt so that I do not really want energy
minimization or geometry optimization to be done on it. Although I set
"none" for "geometry optimization" in GUI, it unfortunately changed the
ligand conformation.

Thank you,
Mengbin


On Thu, Jun 13, 2013 at 2:52 PM, Mengbin Chen <mengbinc at sas.upenn.edu>wrote:

> Dear Dr. Dias,
>
> I tried the command line in Terminal, but Elbow still regularized the
> conformation and bonds of the ligand and the result turned out to be the
> same with that I ran thorough GUI. The thing is that the input pdb file has
> a conformation the ligand should adopt so that I do not really want energy
> minimization or geometry optimization to be done on it. Although I set
> "none" for "geometry optimization" in GUI, it unfortunately changed the
> ligand conformation.
>
> Thank you,
> Mengbin
>
>
> On Thu, Jun 13, 2013 at 2:42 PM, Joao Dias <joao.dias at heptares.com> wrote:
>
>>  Dear Mengbin,
>> You can open a terminal window and run elbow as a command line.
>>
>> phenix.elbow --final_geometry input_file.pdb****
>>
>>
>>  Do not forget to initialize the phenix environment, depending on your
>> terminal shell, one example is:
>> source
>> /Applications/PHENIX-dev-1320/Contents/phenix-dev-1320/phenix_env.sh
>>
>>  All the best,
>> Joao
>>
>>   Dr Joao Dias****
>>
>> Principal Scientist****
>>
>> ** **
>>
>> Heptares Therapeutics Ltd****
>>
>> BioPark, Broadwater Road,****
>>
>> Welwyn Garden City,****
>>
>> Herts, AL7 3AX****
>>
>> UK
>>
>>   From: Mengbin Chen <mengbinc at sas.upenn.edu>
>> Reply-To: PHENIX user mailing list <phenixbb at phenix-online.org>
>> Date: Thursday, 13 June 2013 19:32
>> To: PHENIX user mailing list <phenixbb at phenix-online.org>
>> Subject: [phenixbb] elbow
>>
>>   Dear PHENIX Users,
>>
>>  I have been playing around with Elbow for a while, but I kept having
>> problems generating .cif file. For "Chemical file type" and "Template PDB
>> file", I used the pdb file of the ligand. Since the coordinates in the pdb
>> file corresponds to a conformation desired, I chose "None" for "geometry
>> optimization". After running Elbow, the output pdb file was completely
>> different than the input one -- even double bonds became single bonds and
>> 10-membered ring conformation changed. I have tried Sketcher in CCP4
>> package, but no good results either. Could anyone tell me how to do this
>> correctly? Any help is appreciated!
>>
>>  Thank you in advance,
>> Mengbin
>>
>>  --
>> Mengbin Chen
>> Department of Chemistry
>> University of Pennsylvania
>>
>>     [image: www.heptares.com] <http://www.heptares.com><http://www.heptares.com>
>>
>>
>> The information in this e-mail is confidential and may be legally
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>> stated above and should not be copied or disclosed to any other. If you
>> have received this transmission in error, please make no use of its
>> contents and contact the sender. Contact and registered office address:
>> Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden
>> City, Hertfordshire, AL7 3AX. Company No: 06267989
>>
>>
>
>
> --
> Mengbin Chen
> Department of Chemistry
> University of Pennsylvania
>



-- 
Mengbin Chen
Department of Chemistry
University of Pennsylvania
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