On Tue, Jul 12, 2016 at 12:39 PM, R. Gasper-Schönenbrücher <raphael.gasper@bph.rub.de> wrote:

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<MET 1>.A<N 1> 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

Hi,

AmberTools16 has renamed the forcefields (for example, leaprc.ff14SB is renamed to leaprc.protein.ff14SB).

Please see http://ambermd.org/doc12/Amber16.pdf (page 33, Molecular mechanics force ﬁelds) for further info.

It's likely that AmberPrep has not updated yet.

Hai

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

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