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 ([email protected]) ------------------------------------------------------------------------------ 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 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Sun, Mar 31, 2019 at 2:12 AM 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 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-SMILE...

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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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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Thu, Apr 4, 2019 at 7:59 AM Nigel Moriarty 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Wed, Apr 3, 2019 at 10:44 PM Ahmad Khalifa 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@luxor bin]$ phenix.elbow taxol.pdb

------------------------------------------------------------------------------ electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.14-3260 None - Nigel W. Moriarty ([email protected])

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

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 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Sun, Mar 31, 2019 at 2:12 AM 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 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-SMILE...

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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