Re: [AMBER] python error when using pdb4amber

From: Jason Swails <>
Date: Mon, 18 Jan 2016 16:24:04 -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

‚ÄčIt looks like one of the input files (1EMA.pdb) doesn't exist... Are you
sure you are running this in the same directory that contains 1EMA.pdb?
And that the PDB file has that name?


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Jan 18 2016 - 13:30:04 PST
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