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.
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.