Thanks Jason, I didn't source the amber.sh!
Elisa
On Tue, Jan 19, 2016 at 3:00 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Jan 18, 2016 at 7:34 AM, Elisa Pieri <elisa.pieri90.gmail.com>
> wrote:
>
>> Dear all,
>>
>> I know that my problem is more technical and (apparently) concerns my
>> python libraries, but I could not find anything helping online. I
>> successfully installed AmberTools15, and everything seems to work
>> fine. I am following the tutorial B5, but at the very first step, when
>> I try to use the pdb4amber, I get this error:
>>
>> elisa.agachon:~/tutorials$ /home/elisa/amber14/bin/pdb4amber -i
>> 1EMA.pdb -o gfp.pdb --dry --reduce
>> Traceback (most recent call last):
>> File "/home/elisa/amber14/bin/pdb4amber", line 904, in <module>
>> opt.constantph, opt.mostpop, opt.reduce, opt.model)
>> File "/home/elisa/amber14/bin/pdb4amber", line 807, in run
>> stdout=subprocess.PIPE, stderr=subprocess.PIPE)
>> File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
>> errread, errwrite)
>> File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
>> raise child_exception
>> OSError: [Errno 2] No such file or directory
>>
>
> I was wrong in my initial diagnosis. This error is not caused when the
> PDB file does not exist. It is caused when the "reduce" program is not
> installed and/or cannot be found:
>
> $ which reduce
> which: no reduce in
> [snip path]
>
> $ pdb4amber -i 3ptb.pdb --reduce
> Traceback (most recent call last):
> File "/usr/local/amber14/bin/pdb4amber", line 904, in <module>
> opt.constantph, opt.mostpop, opt.reduce, opt.model)
> File "/usr/local/amber14/bin/pdb4amber", line 807, in run
> stdout=subprocess.PIPE, stderr=subprocess.PIPE)
> File "/usr/lib64/python2.7/subprocess.py", line 710, in __init__
> errread, errwrite)
> File "/usr/lib64/python2.7/subprocess.py", line 1335, in _execute_child
> raise child_exception
> OSError: [Errno 2] No such file or directory
>
> Do you have $AMBERHOME/bin added to your PATH? This seems to be required
> for using reduce with pdb4amber (I will adjust the behavior so it takes
> reduce from AMBERHOME instead for future versions).
>
> So my advice here:
>
> 1. Make sure $AMBERHOME/bin/reduce exists
> 2. Make sure you run the command "source $AMBERHOME/amber.sh" somewhere.
> Either put it in your .bashrc file or, alternatively, run the command in
> any shell you wish to run Amber in.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 21 2016 - 01:30:03 PST
