[phenixbb] Amber in phenix
nwmoriarty at lbl.gov
Tue Jul 12 12:36:05 PDT 2016
Hai is correct about Phenix not supporting AmberTools16. I have been
testing the code to support it and plan on releasing it in a short time
frame. I suggest you install AmberTools15 for use with Phenix or wait until
the code is updated.
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
On Tue, Jul 12, 2016 at 10:01 AM, Hai Nguyen <nhai.qn at gmail.com> wrote:
> 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
>> 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
> 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.
>> 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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