protein pKas?

User 21b7e0228c

16-12-2005 14:31:55

I was just wondering how far one may go with the pKa predictor and got myself a mini-protein from the pdb (see attached .sdf obtained via molconverter from the downloaded pdb). Then I tried my small hydrogen-setting prog, which works fine for small molecules.... and KRASH (java.lang.RuntimeException: Molecule@787171 is not a parent of child S-group SuperatomSgroup@15fea60 - I'm still in v 3.5!)! It breaks at plugin.setMol(inMol) - is it too big? Can this be fixed easily? I don't expect the pKa plugin to account for through-space interactions and dielectric effects, but to recognize lysines, arginines and COO- and set their protons properly (that's more than many other programs are able to!) My goal is to later teach the routine to recognize "false" C and N-termini resulting from cuts through the peptide chain around the active site and NOT to charge those atoms, while nevertheless charging the sidechains and the real N/C termini. Feasible?

ChemAxon fb166edcbd

16-12-2005 19:47:55

I will look at this on Monday (19 Dec).

ChemAxon fb166edcbd

19-12-2005 17:12:27

It seems that this sgroup-bug has disappeared in the latest JChem:

JChem 3.1.4. I have received the attached result file.