[phenixbb] Ligand woes
rwgrosse-kunstleve at lbl.gov
Tue Jul 5 07:23:12 PDT 2011
Could you send me (off-list) the fragment from your PDB file with the
Could you also let me know the phenix version number of your installation?
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.
> 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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> phenixbb at phenix-online.org
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