[phenixbb] Amber in phenix

Hi all, I am trying to run amber from phenix with a standard pdb file, no co-factors etc and struggle already at the phenix.AmberPrep script. For unknown reasons, the .prmtop file stays empty (0 bytes). I have tried to figure out from the amber python scripts, where the problem might be, but didn't find anything obvious (the "self.ns_names" variable stays empty) The leap log files states two problems: 1) ......Nonterminal, was not found in name map. (for every single amino acid) 2) FATAL: Atom .R.A does not have a type. (for every single atom) which ends up in: "Failed to generate parameters Parameter file was not saved." There is no .map2 file generated. Phenix version: dev-2463 Amber: Ambertools 16 Every help is highly appreciated. Many thanks! Best, Raphael -- Raphael Gasper-Schönenbrücher Universität Bochum AG Proteinkristallographie, Lehrstuhl für Biophysik, NDEF 04/316 Universitätsstraße 150 44801 Bochum Germany Tel: +49 (0)234-32 27086 Fax: +49 (0)234-32 14762