[phenixbb] Phenix elbow taxol

Nigel Moriarty nwmoriarty at lbl.gov
Thu Apr 4 08:02:43 PDT 2019


I forgot to mention that there is a YouTube tutorial on LigandFit.

https://www.youtube.com/watch?v=hLr4owC1pTA

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


On Thu, Apr 4, 2019 at 7:59 AM Nigel Moriarty <nwmoriarty at lbl.gov> wrote:

> Your problems arise from not having the same atom names in the model and
> the restraints. I suggest you use the PDB and/or restraints I sent and fit
> it into the model. This can be done several ways but Phenix has the
> LigandFit program for just such a task. Once you fit the taxol from the PDB
> and/or restraints (you can supply both to LigandFit and the restraints are
> the best choice) you will not see the same problem.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>
>
> On Wed, Apr 3, 2019 at 10:44 PM Ahmad Khalifa <underoath006 at gmail.com>
> wrote:
>
>> Thanks a lot Nigel. I can generate the restraint file using chemical
>> component TA1 and SDF file. However, after doing some testing, the input
>> ligand should have the same coordinates as in my PDB, otherwise real space
>> refienemnt complains by saying "unknown nonbonded energy type symbols",
>> which I'm guessing doesn't match the restraint file to my ligand.
>>
>> I tried running elbow on the REattached pdb, I couldn't generate the
>> restraint file (Error: Sorry: Unable to determine the bonding):
>>
>> [labusr at luxor bin]$ phenix.elbow taxol.pdb
>>
>>  ------------------------------------------------------------------------------
>>   electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.14-3260
>> None
>>     - Nigel W. Moriarty (NWMoriarty at LBL.Gov)
>>
>>  ------------------------------------------------------------------------------
>>
>>  Random number seed:  3628800
>>  Initial processing time : 0.00 seconds
>>  0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing
>> Parsing P
>>
>> Input format is PDB
>>
>> MoleculeClass :  C:43  N: 1  O:14 (PDB format)
>> 58 atoms
>> 63 bonds
>> 0 angles
>> 0 dihedrals
>> 0 rings
>> 0 chirals
>>  Predicted memory usage by semi-empirical method : 78Mb
>>  Timing estimates
>>      Python portion         / ATP : 275%
>>      c++ optimisation cycle / ATP : 817%
>>  0:00 Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise
>> Bondise B
>>
>>     Failed to determine the bonding of a fragment of the molecule.
>>
>>     PDB file elbow.taxol_pdb.001.pdb written.
>>     Bonding file elbow.taxol_pdb.001.bonding.py written.
>>
>>     Edit bonding file to reflect the desired bond.
>>
>>
>>
>>     ALTERNATIVELY
>>
>>     Re-run eLBOW with the --reel option and the molecule wil be loaded
>>     into REEL.  Edit the bonds and save the results as "fixed.cif" to
>>     allow eLBOW to load the bonding.
>>
>>     You can also use a pull-down menu to push to eLBOW.
>>
>> Sorry: Unable to determine the bonding
>>
>> I tried to superimpose the SDF to my structure but I think there are some
>> differences in the structure, and number of atoms so the superimposition
>> didn't work. i would appreciate if soemone can help me generate restraint
>> of the attached PDB.
>>
>> On Mon, Apr 1, 2019 at 12:35 PM Nigel Moriarty <nwmoriarty at lbl.gov>
>> wrote:
>>
>>> Ahmed
>>>
>>> Taxol is quite tricky so using the chemical components option is a
>>> choice that provides more information than the SMILES.
>>>
>>> phenix.elbow --chemical_components=TA1
>>>
>>> I have attached the files.
>>>
>>> Cheers
>>>
>>> Nigel
>>>
>>> ---
>>> Nigel W. Moriarty
>>> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>>> Lawrence Berkeley National Laboratory
>>> Berkeley, CA 94720-8235
>>> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
>>> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>>>
>>>
>>> On Sun, Mar 31, 2019 at 2:12 AM <r.joosten at nki.nl> wrote:
>>>
>>>> Before you make restraints yourself, check whether it is already in the
>>>> dictionary. The name should be TA1 (
>>>> http://ligand-expo.rcsb.org/reports/T/TA1/index.html).
>>>>
>>>> Cheers,
>>>> Robbie
>>>>
>>>> On 31 Mar 2019 10:45, Georg Mlynek <georg.mlynek at univie.ac.at> wrote:
>>>>
>>>> Dear Ahmad, one way is to use the smiles string. If taxol if also named
>>>> Paclitaxel then here it is:
>>>>
>>>>
>>>> https://pubchem.ncbi.nlm.nih.gov/compound/paclitaxel#section=Canonical-SMILES
>>>>
>>>> Then just watch this video on phenix.elbow
>>>>
>>>> https://www.youtube.com/watch?v=8qVYTUVKlbQ
>>>>
>>>> Br, Georg.
>>>>
>>>>
>>>> On 31.03.19 08:08, Ahmad Khalifa wrote:
>>>> How can I generate restraint files for taxol?
>>>>
>>>> I attached my taxol.pdb for reference.
>>>>
>>>> Thanks.
>>>>
>>>>
>>>>
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