[phenixbb] Phenix elbow taxol

Thu Apr 4 08:00:26 PDT 2019

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.
>>>
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> Unsubscribe: phenixbb-leave at phenix-online.org<mailto:
>>> phenixbb-leave at phenix-online.org>
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20190404/c36d3b77/attachment-0001.htm>