Lionel
- bond outlier CAD - OAC model 1.26 - ideal: ProDRG single 1.36, readyset deloc 1.30, eLBOW deloc 1.429, smiles deloc 1.269 - bond outlier CBC - OBD model 1.30 - ideal: ProDRG deloc 1.23, readyset double 1.23, eLBOW aromatic 1.768, smiles double 1.234 - angle outlier CAG CAF CAD model 99 - ideal: ProDRG 111, readyset 117, eLBOW 109, smiles 117 - dihedral outlier CBC NBB CAY CAZ model 2.2 - ideal: ProDRG 180, readyset 131.66, eLBOW 62.5, smiles 68
It seems to me that chemistry clearly depends on the software used, amazing.
This shouldn't be a huge surprise - the programs use different methods to specify (or guess) molecule parameters, some of which are more effective than others, and different approximations when optimizing the geometry, most of which are optimized for speed rather than theoretical rigor (unless you are running quantum chemical calculations like the AM1 optimization in eLBOW). As a general rule, it is very difficult to accurately guess the chemistry of a molecule based on a PDB file alone; I suspect that CIFs may have similar problems, but Nigel can clarify.
All ligand programs are parameterising the geometry (and chemistry) of a ligand to use in a refinement. This procedure relies greatly on the quality of the input, so you need to give it the best quality input to get the best parameterisation of the chemistry. As Nat said, SMILES strings are a high quality input and you can add value but using AM1 (--opt). CIF restraints file have all the information for good parameterisation but can more easily contains errors so are less reliable. The most unreliable is a PDB input so many programs need to make assumptions in order to generate restraints. The differences between eLBOW and ReadySet! are due to different inputs. eLBOW is the engine of ligand restraints generation so its used in ReadySet!, however, different inputs are used because the model has a set of PDB atoms and a three-letter residue code. If the code is in the PDB ligand database, Chemical Components (CC), things go well because ReadySet! can draw on the information in the CC to generate the restraints. If the code in not in the CC or some other catastrophic mismatch between ligand code and atom names, ReadySet! uses the only information available, the PDB lines of the ligand. This is not the best situation so running eLBOW directly is a better choice. I'm happy to take a closer look if you send me the files directly. Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov