[phenixbb] Amber in phenix

R. Gasper-Schönenbrücher raphael.gasper at bph.rub.de
Tue Jul 12 09:39:42 PDT 2016

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 
2) FATAL:  Atom .R<MET 1>.A<N 1> does not have a type. (for every single 
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!

Raphael Gasper-Schönenbrücher
Universität Bochum
AG Proteinkristallographie, Lehrstuhl für Biophysik, NDEF 04/316
Universitätsstraße 150
44801 Bochum
Tel: +49 (0)234-32 27086
Fax: +49 (0)234-32 14762

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