On Mon, Oct 26, 2015 at 10:29 AM, Hadeer ELHabashy <
hadeer.elhabashi.gmail.com> wrote:
> that is what exactly I have done
>
> I uninstalled AMBER and replaced AmberTools13 with AmberTool15
> then I did " make clean " and I reinstalled AMBER12 along side with
> AmberTools15 together.
>
In the same directory? What is the full path of pmemd? What is the full
path of parmed.py from AmberTools 15?
> and by the way, when I ran my command, parmed started to work
>
> _____
> __...---'-----`---...__
> _===============================
> ______________,/' `---..._______...---'
> (______________). . ,--'
> / /.---' `. /
> '--------_ - - - - _/ P A R M E D
> `~~~~~~~~'
>
> ParmEd: a Parameter file Editor
>
> but it stopped then due to this error I sent before .
> I think that is saying " ParmEd can run .
>
The error you printed was showing that source code that *only exists* in
AmberTools 15 was present in a directory called amber12. The only way I
can think that this could have happened is that you unpacked
AmberTools15.tar.bz2, renamed "amber14" to "amber12", then unpacked
Amber12.tar.bz2 into the same directory. Or something similar to that.
As I said in my last email, *you can't do this* and expect it to work. I
made an entire webpage to help describe how to install AmberTools 15
alongside an older version of Amber.
If this is not what you did, then you will have to help me understand how
AmberTools 15 modules became installed to an Amber 12 source tree. Because
that should never happen.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Oct 26 2015 - 09:30:03 PDT
