[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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