[phenixbb] Amber module in phenix on Ubuntu 18.04

Guenter Fritz guenter.fritz.phenix.ccp4 at gmail.com
Thu Jun 4 13:53:11 PDT 2020


  Nigel,

thanks a lot. Overall, if Ubuntu is not ready yet, then I will simply 
use a Centos box, no problem.
Just a note: I checked also another Ubuntu box to rule out individual 
problems. The refinement crashes, here, e.g. I used the example of your 
webinar
/
/
/$ phenix.refine 4phenix_1a0b.pdb use_amber=True \ //
//>     amber.topology_file_name=4amber_1a0b.prmtop \ //
//>     amber.coordinate_file_name=4amber_1a0b.rst7 \ //
//>     amber.order_file_name=4amber_1a0b.order \ //
//> 1a0b.mtz //
/ /
//Could not import the compiled Python-sander interface. Make sure you 
have the Python development libraries installed and that you have 
sourced amber.sh or amber.csh# Date 2020-06-04 Time 11:26:08 CEST +0200 
(1591262768.33 s) //
//#phil __OFF__ //
/ /..... //
//Processing inputs. This may take a minute or two. //
//Sorry: Unknown command line parameter definition: use_amber = True/
/
/
/Best regards,/
/Guenter
/
/
/
> Guenter
>
>     I cannot get the Amber and AFITT menu bars in the phenix.refine
>     GUI on a  Ubuntu (Xubuntu 18.04) box.
>
> Do you have AFITT installed and setup following 
> https://www.phenix-online.org/documentation/reference/afitt.html
>
I  have overlooked that. I usually install it an all machines, but 
forget this one.
> Regarding Amber,  Ubuntu is the problem child for many things 
> including Phenix-Amber. I'm hoping Billy can help here.
>
>      I set Preferences "Enable alpha-test programs and features" 
>     (works on my Mac 10.14.6 and SciLinux6 box ).
>
> Don't think this matters for Amber anymore as it's distributed with 
> Phenix.
>
>
>     Moreover, on the Xubuntu machine: when I start the phenix.refine
>     GUI (phenix version 1.18.2-3874) I see the following error message
>     in the terminal running phenix:
>
>     //$ phenix//
>
>     /Could not import the compiled Python-sander interface. Make sure
>     you have the Python development libraries installed and that you
>     have sourced amber.sh or amber.csh
>     /
>
> Does it crash? Billy probably has the answers here.
>
>     //
>
>
>     //------------------------//
>
>     python 3.7 is installed and python development tools :/
>     /
>
>     /------------------------
>     /
>
>     /$ python -V //
>     //Python 3.7.6 /
>
>     /$ sudo apt list -a   python3.7-dev //
>     //Listing... Done //
>     //python3.7-dev/bionic-updates,now 3.7.5-2~18.04 amd64 [installed] //
>     //python3.7-dev/bionic-security 3.7.3-2~18.04.1 amd64 //
>     //python3.7-dev/bionic 3.7.0~b3-1 amd64
>     /
>
>     /------------------------/
>
> Phenix 1.18.2 should be the last major release to use Python2 so you 
> need to have it available.

> Nigel


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