[phenixbb] Amber in phenix

[Nigel Moriarty]

Raphael

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.

Cheers

Nigel

---
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
>> 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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>
>
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