[phenixbb] Amber in phenix

[Hai Nguyen]

On Tue, Jul 12, 2016 at 12:39 PM, R. Gasper-Schönenbrücher <
raphael.gasper at 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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