[phenixbb] Ligand woes

[Ralf Grosse-Kunstleve]

Hi Jose,

Could you send me (off-list) the fragment from your PDB file with the
two ligands?

Could you also let me know the phenix version number of your installation?

Ralf


On Tue, Jul 5, 2011 at 5:53 AM, José Trincão <trincao at dq.fct.unl.pt> wrote:
> Hello all,
> I have been having very weird problems refining a structure with several ligands. The weirdest problem is that if I try to run ligand fit giving just the name of the ligands, no problem - it finds the ligands (FAD and MTE). I save the pdb with all the ligands in and phenix.refine complains that MTE is not recognised, I have to run ready-set. I do it. Run phenix.refine again, and now it complains with the following:
>  Number of atoms with unknown nonbonded energy type symbols: 116
>   "HETATM18439  C1' MTE A3003 .*.     C  "
>   "HETATM18441  C2' MTE A3003 .*.     C  "
>   "HETATM18443  C3' MTE A3003 .*.     C  "
>   "HETATM18444  O3' MTE A3003 .*.     O  "
>   "HETATM18474  N9A FAD A3005 .*.     N  "
>   "HETATM18475  C8A FAD A3005 .*.     C  "
>   "HETATM18476  N7A FAD A3005 .*.     N  "
>   "HETATM18477  C5A FAD A3005 .*.     C  "
>   "HETATM18478  C6A FAD A3005 .*.     C  "
>   "HETATM18480  N1A FAD A3005 .*.     N  "
>   ... (remaining 106 not shown)
>
> Any help will be greatly appreciated.
>
> Jose
>
>
> José Trincão, PhD       CQFB at FCT-UNL
> 2829-516 Caparica, Portugal
>
> "It's very hard to make predictions... especially about the future" - Niels Bohr
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