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@luxor bin]$ phenix.elbow taxol.pdb 

 ------------------------------------------------------------------------------

  electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.14-3260 None

    - Nigel W. Moriarty (NWMoriarty@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@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@LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Sun, Mar 31, 2019 at 2:12 AM <r.joosten@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@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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