Re: [AMBER] python error when using pdb4amber

From: Jason Swails <>
Date: Tue, 19 Jan 2016 09:00:46 -0500

On Mon, Jan 18, 2016 at 7:34 AM, Elisa Pieri <>

> 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/", line 710, in __init__
> errread, errwrite)
> File "/usr/lib/python2.7/", 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/", line 710, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.7/", 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/" somewhere.
Either put it in your .bashrc file or, alternatively, run the command in
any shell you wish to run Amber in.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jan 19 2016 - 06:30:03 PST
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